UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549   FORM 20-F/A (Amendment No. 1)   (Mark One)  ☐
REGISTRATION STATEMENT PURSUANT TO SECTION 12(b) or (g) OF THE SECURITIES EXCHANGE ACT OF 1934 OR  ☒
ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2018 OR  ☐
TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 OR  ☐
SHELL COMPANY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Commission file number 001-36891   CELLECTIS S.A. (Exact
name of Registrant as specified in its charter and translation of Registrants name into English)   France (Jurisdiction of incorporation or organization) Cellectis S.A. 8, rue
de la Croix Jarry 75013 Paris, France (Address of principal executive office) Marie-Bleuenn Terrier General Counsel Cellectis S.A. 8, rue de
la Croix Jarry 75013 Paris, France Tel: +33 (0)1 81 69 16 00, Fax: +33 (0)1 81 69 16 06 E-mail: marie-bleuenn.terrier@cellectis.com (Name, Telephone, E-mail and/or Facsimile number and Address of Company Contact Person) Securities registered or to be registered pursuant to Section 12(b) of the Act.  Title of each class

Name of each exchange on which
registeredAmerican Depositary Shares, each representing one

Nasdaq Global Marketordinary share, nominal value 0.05 per shareOrdinary shares, nominal value 0.05 per share*

Nasdaq Global Market*  *
Not for trading, but only in connection with the registration of the American Depositary Shares. Securities registered or to be registered pursuant to Section 12(g) of the Act. None Securities for
which there is a reporting obligation pursuant to Section 15(d) of the Act. None   Indicate the number of outstanding shares of each of the issuers classes of capital or common stock as of the close of the period covered
by the Annual Report. Ordinary shares, nominal value 0.05 per share: 42,430,069 as of December 31, 2018   Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities
Act.    Yes   ☐    No   ☒ If this report is an annual or transition
report, indicate by check mark, if the registrant is not required to file reports pursuant to Section 13 or 15(d) of the Securities Exchange Act of
1934.    Yes   ☐    No   ☒ Note  Checking the box above will not
relieve any registrant required to file reports pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 from their obligations under those Sections. Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act
of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90
days.    Yes   ☒    No   ☐ Indicate by check mark whether the
registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the
registrant was required to submit such files).    Yes   ☒    No   ☐ Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, or a non-accelerated
filer. See definition of accelerated filer and large accelerated filer in Rule 12b-2 of the Exchange Act.  Large accelerated filer

☒

Accelerated filer

☐Non-accelerated filer

☐

Emerging Growth Company

☐ If an emerging growth company that prepares its financial statements in accordance with U.S. GAAP, indicate by check mark if
the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13 (a) of the Exchange Act.   ☐  
The term new or revised financial accounting standard refers to any update issued by the Financial
Accounting Standards Board to its Accounting Standards Codification after April 5, 2012. Indicate by check mark which basis of
accounting the registrant has used to prepare the financial statements included in this filing:  U.S. GAAP   ☐



International Financial Reporting Standards as issued
by the International Accounting Standards Board  ☒

Other   ☐ If Other has been checked in response to the previous question, indicate by check mark which financial statement
item the registrant has elected to follow:    Item 17   ☐    Item 18   ☐ If this is an annual report, indicate by check mark whether the registrant is a shell company (as defined in Rule
12b-2 of the Exchange Act).    Yes   ☐    No   ☒ (APPLICABLE ONLY TO ISSUERS INVOLVED IN BANKRUPTCY PROCEEDINGS DURING THE PAST FIVE YEARS) Indicate by check mark whether the registrant has filed all documents and reports required to be filed by Sections 12, 13 or 15(d) of the Securities Exchange
Act of 1934 subsequent to the distribution of securities under a plan confirmed by a court.    ☐  Yes    ☐   No




---

EXPLANATORY NOTE Cellectis, S.A. (the Company) hereby amends its Annual Report on Form 20-F for the fiscal
year ended December 31, 2018 (the Annual Report) through the filing of this Amendment No. 1 (this Amendment) solely for the purpose of re-filing Exhibits 4.25 and 4.26
(together, the Exhibits) in accordance with guidance published by the staff (the Staff) of the Securities and Exchange Commission (the SEC) relating to the filing of redacted material contracts without applying
for confidential treatment of the redacted information (the Staff Guidance), as provided for in the SECs Release No. 33-10618, which became effective on April 2, 2019, and the
amendments to Form 20-F provided for therein (the New CT Rules). In accordance with the Staff Guidance, the Company has withdrawn its pending confidential treatment application with respect to the
Exhibits and is, through the filing of this Amendment, re-filing the Exhibits in accordance with the requirements of the New CT Rules. The footnotes to the index of exhibits included in this Amendment have
also been revised to distinguish exhibits that reflect omissions pursuant to confidential treatment orders previously granted by the Staff and omissions made in accordance with the New CT Rules. Except for the revised Exhibits, this Amendment does not amend, update or restate any other items or sections of the Annual Report and does
not reflect events occurring after the original filing date of the Annual Report. In connection with the filing of this Amendment, the
Company is including certifications of the Companys Chief Executive Officer and Chief Financial Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the
Securities Exchange Act of 1934, as amended (the Exchange Act).




---

ITEM 19.
EXHIBITS The following exhibits are filed as part of this Annual Report:  ExhibitNumber

Description of Exhibit

Schedule/Form

File
Number

Exhibit

File Date1.1#

By-laws (status) of the registrant (English translation)

20-F

001-36891

1.1

March 12, 20192.1#

Form of Deposit Agreement

F-1

333-202205

4.1

March 10, 20152.2#

Form of American Depositary Receipt (included in Exhibit 2.1)

F-1

333-202205

Included in 4.1

March 10, 20154.1#

Patent License Agreement #C-00061901 between LInstitut Pasteur and Cellectis S.A., dated June 19, 2000 (English translation)

20-F

001-36891

4.1

March 12, 20194.1.1#

Amendment No. 1 to Patent License Agreement #C-00061901 between LInstitut Pasteur and Cellectis S.A., dated December 20, 2002 (English translation)

20-F

001-36891

4.1.1

March 12, 20194.1.2#

Amendment No. 2 to Patent License Agreement #C-00061901 between LInstitut Pasteur and Cellectis S.A., dated September 8, 2003 (English translation)

20-F

001-36891

4.1.2

March 12, 20194.1.3#

Amendment No. 3 to Patent License Agreement #C-00061901 between LInstitut Pasteur and Cellectis S.A., dated February 26, 2008

F-1

333-202205

10.1.3

March 12, 20154.1.4#

Amendment No. 4 to Patent License Agreement #C-00061901 between LInstitut Pasteur and Cellectis S.A., dated April 11, 2013 (English translation)

F-1

333-202205

10.1.4

March 12, 20154.2#

Patent License Agreement #C-00061906 between LInstitut Pasteur and Cellectis S.A., dated October 19, 2000 (English translation)

20-F

001-36891

4.2

March 12, 20194.2.1#

Amendment No. 1 to Patent License Agreement #C-00061906 between LInstitut Pasteur and Cellectis S.A., dated September 8, 2003 (English translation)

20-F

001-36891

4.2.1

March 12, 20194.2.2#

Amendment No. 2 to Patent License Agreement #C-00061906 between LInstitut Pasteur and Cellectis S.A., dated June 24, 2004 (English translation)

20-F

001-36891

4.2.2

March 12, 20194.2.3#

Amendment No. 3 to Patent License Agreement #C-00061906 between LInstitut Pasteur and Cellectis S.A., dated August 24, 2005 (English translation)

20-F

001-36891

4.2.3

March 12, 20194.2.4#

Amendment No. 4 to Patent License Agreement #C-00061906 between LInstitut Pasteur and Cellectis S.A., dated December 27, 2007 (English translation)

20-F

001-36891

4.2.4

March 12, 2019




---

ExhibitNumber

Description of Exhibit

Schedule/Form

File Number

Exhibit

File Date4.3#

Patent License Agreement #C-00061905 between LInstitut Pasteur and Cellectis S.A., dated June 19, 2000 (English translation)

20-F

001-36891

4.3

March 12, 20194.3.1#

Amendment No. 1 to Patent License Agreement #C-00061905 between LInstitut Pasteur and Cellectis S.A., dated September 8, 2003 (English translation)

20-F

001-36891

4.3.1

March 12, 20194.4

[Reserved]4.4.1

[Reserved]4.5

[Reserved]4.5.1

[Reserved]4.6#*

Exclusive Patent License Agreement between Regents of the University of Minnesota and Cellectis S.A., dated January 10, 2011

F-1

333-202205

10.6

March 12, 20154.6.1#*

First Amendment to the Exclusive Patent License Agreement between Regents of the University of Minnesota and Cellectis S.A., dated May 24, 2012

F-1

333-202205

10.6.1

March 12, 20154.6.2#*

Second Amendment to the Exclusive Patent License Agreement between Regents of the University of Minnesota and Cellectis S.A., dated May 27, 2014

F-1

333-202205

10.6.2

March 12, 20154.6.3#*

Third Amendment to the Exclusive Patent License Agreement between Regents of the University of Minnesota and Cellectis S.A., dated December 16, 2015

20-F

001-36891

4.6.3

March 13, 20184.7#

Patent & Technology License Agreement between Ohio State Innovation Foundation and Cellectis S.A., dated October 23, 2014

20-F

001-36891

4.7

March 12, 20194.8#

Warrants Issue Agreement between Cellectis S.A. and Kepler Capital Markets SA, dated December 20, 2012 (English translation)

F-1

333-202205

10.8

March 10, 20154.8.1#

First Amendment to Warrants Issue Agreement between Cellectis S.A. and Kepler Capital Markets SA, dated June 6, 2013 (English translation)

F-1

333-202205

10.8.1

March 10, 20154.8.2#

Second Amendment to Warrants Issue Agreement between Cellectis S.A. and Kepler Capital Markets SA, dated October 7, 2013 (English translation)

F-1

333-202205

10.8.2

March 10, 20154.9#

Warrant Agreement between Cellectis S.A. and Trout Capital LLC, dated March 24, 2014

F-1

333-202205

10.9

March 10, 20154.10#

Change of Control Plan, effective as of September 4, 2014 (English translation)

F-1

333-202205

10.10

March 10, 2015




---

ExhibitNumber

Description of Exhibit

Schedule/Form

File Number

Exhibit

File Date4.11#

Summary of BSA Plan

F-1

333-202205

10.11

March 10, 20154.12#

Summary of BSPCE Plan

F-1

333-202205

10.12

March 10, 20154.13#

2012 Free Share Plan

F-1

333-202205

10.13

March 10, 20154.14#

2013 Free Share Plan

F-1

333-202205

10.14

March 10, 20154.15#

2014 Free Share Plan

F-1

333-202205

10.15

March 10, 20154.16#

2015 Free Share Plan

20-F

001-36891

4.16

March 21, 20164.17#

2015 Stock Option Plan

20-F

001-36891

4.17

March 21, 20164.18#

2016 Stock Option Plan

S-8

333-214884

99.1

December 2, 20164.19#

2017 Stock Option Plan

S-8

333-222482

99.1

January 9, 20184.20#

Summary of BSA Plan

S-8

333-222482

99.2

January 9, 20184.21#

Free Share 2018 Plan

S-8 POS

333-222482

99.3

April 13, 20184.22#

2018 Stock Option Plan

S-8

333-227717

99.1

October 5, 20184.23#

Summary of BSA Plan

S-8

333-227717

99.2

October 5, 20184.24#

Second Free Share 2018 Plan

S-8

333-227717

99.3

October 5, 20184.25**

License Agreement Between Allogene Therapeutics, Inc. and Cellectis S.A. dated March 8, 2019







Filed herewith4.26**

License, Development and Commercialization Agreement between Les Laboratoires Servier and Cellectis S.A. dated March 6, 2019







Filed herewith4.27#

Management Services Agreement between Cellectis S.A., Cellectis, Inc. and Calyxt, Inc. dated as of January 1, 2016

20-F

001-36891

4.27

March 12, 20194.28#

Management Services Agreement Amendment dated July 25, 2017 between Cellectis S.A. and Calyxt, Inc.

20-F

001-36891

4.28

March 12, 20194.29#

Separation Agreement dated July 25, 2017 between Cellectis S.A. and Calyxt, Inc.

20-F

001-36891

4.29

March 12, 20194.30#

Stockholders Agreement dated July 25, 2017 between Cellectis S.A. and Calyxt, Inc.

20-F

001-36891

4.30

March 12, 20194.31#

License Agreement dated July 25, 2017 between Cellectis S.A. and Calyxt, Inc.

20-F

001-36891

4.31

March 12, 2019




---

ExhibitNumber

Description of Exhibit

Schedule/Form

File Number

Exhibit

File Date8.1#

List of subsidiaries of the registrant

20-F

001-36891

8.1

March 12, 201912.1

Certificate of Principal Executive Officer pursuant to Securities Exchange Act Rules 13a-14(a) and 15d-14(a) as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002







Filed herewith12.2

Certification by the Principal Financial Officer pursuant to Securities Exchange Act Rules 13a-14(a) and 15d-14(a) as adopted pursuant to
Section 302 of the Sarbanes-Oxley Act of 2002







Filed herewith13.1#

Certification by the Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

20-F

001-36891

13.1

March 12, 201913.2#

Certification by the Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

20-F

001-36891

13.2

March 12, 201915.1#

Consent of Ernst & Young et Autres

20-F

001-36891

15.1

March 12, 2019  
Indicates a management contract or any compensatory plan, contract or arrangement. #
Indicates a document previously filed with the Commission. *
Confidential treatment has been granted with respect to certain portions of this exhibit (indicated by
asterisks). Omitted portions have been filed separately with the Securities and Exchange Commission. **
Portions of this exhibit (indicated by asterisks) have been omitted in accordance with the rules of the
Securities and Exchange Commission.




---

EXHIBIT INDEX The following exhibits are filed as part of this Annual Report:  ExhibitNumber

Description of Exhibit

Schedule/
Form

File
Number

Exhibit

File Date1.1#

By-laws (status) of the registrant (English translation)

20-F

001-36891

1.1

March 12, 20192.1#

Form of Deposit Agreement

F-1

333-202205

4.1

March 10, 20152.2#

Form of American Depositary Receipt (included in Exhibit 2.1)

F-1

333-202205

Included in 4.1

March 10, 20154.1#

Patent License Agreement #C-00061901 between LInstitut Pasteur and Cellectis S.A., dated June 19,
 2000 (English translation)

20-F

001-36891

4.1

March 12, 20194.1.1#

Amendment No. 
1 to Patent License Agreement #C-00061901 between LInstitut Pasteur and Cellectis S.A., dated December 20, 2002 (English translation)

20-F

001-36891

4.1.1

March 12, 20194.1.2#

Amendment No. 
2 to Patent License Agreement #C-00061901 between LInstitut Pasteur and Cellectis S.A., dated September 8, 2003 (English translation)

20-F

001-36891

4.1.2

March 12, 20194.1.3#

Amendment No. 
3 to Patent License Agreement #C-00061901 between LInstitut Pasteur and Cellectis S.A., dated February 26, 2008

F-1

333-202205

10.1.3

March 12, 20154.1.4#

Amendment No. 
4 to Patent License Agreement #C-00061901 between LInstitut Pasteur and Cellectis S.A., dated April 11, 2013 (English translation)

F-1

333-202205

10.1.4

March 12, 20154.2#

Patent License Agreement #C-00061906 between LInstitut Pasteur and Cellectis S.A., dated October 19,
 2000 (English translation)

20-F

001-36891

4.2

March 12, 20194.2.1#

Amendment No. 
1 to Patent License Agreement #C-00061906 between LInstitut Pasteur and Cellectis S.A., dated September 8, 2003 (English translation)

20-F

001-36891

4.2.1

March 12, 20194.2.2#

Amendment No. 
2 to Patent License Agreement #C-00061906 between LInstitut Pasteur and Cellectis S.A., dated June 24, 2004 (English translation)

20-F

001-36891

4.2.2

March 12, 20194.2.3#

Amendment No. 
3 to Patent License Agreement #C-00061906 between LInstitut Pasteur and Cellectis S.A., dated August 24, 2005 (English translation)

20-F

001-36891

4.2.3

March 12, 20194.2.4#

Amendment No. 
4 to Patent License Agreement #C-00061906 between LInstitut Pasteur and Cellectis S.A., dated December 27, 2007 (English translation)

20-F

001-36891

4.2.4

March 12, 2019




---

ExhibitNumber

Description of Exhibit

Schedule/
Form

File
Number

Exhibit

File Date4.3#

Patent License Agreement #C-00061905 between LInstitut Pasteur and Cellectis S.A., dated June 19,
 2000 (English translation)

20-F

001-36891

4.3

March 12, 20194.3.1#

Amendment No. 
1 to Patent License Agreement #C-00061905 between LInstitut Pasteur and Cellectis S.A., dated September 8, 2003 (English translation)

20-F

001-36891

4.3.1

March 12, 20194.4

[Reserved]4.4.1

[Reserved]4.5

[Reserved]4.5.1

[Reserved]4.6#*

Exclusive Patent License Agreement between Regents of the University of Minnesota and Cellectis S.A., dated January 10, 2011

F-1

333-202205

10.6

March 12, 20154.6.1#*

First Amendment to the Exclusive Patent License Agreement between Regents of the University of Minnesota and Cellectis S.A., dated May 24,
 2012

F-1

333-202205

10.6.1

March 12, 20154.6.2#*

Second Amendment to the Exclusive Patent License Agreement between Regents of the University of Minnesota and Cellectis S.A., dated May 27,
 2014

F-1

333-202205

10.6.2

March 12, 20154.6.3#*

Third Amendment to the Exclusive Patent License Agreement between Regents of the University of Minnesota and Cellectis S.A., dated December 16,
 2015

20-F

001-36891

4.6.3

March 13, 20184.7#

Patent & Technology License Agreement between Ohio State Innovation Foundation and Cellectis S.A., dated October 23, 2014

20-F

001-36891

4.7

March 12, 20194.8#

Warrants Issue Agreement between Cellectis S.A. and Kepler Capital Markets SA, dated December 20, 2012 (English translation)

F-1

333-202205

10.8

March 10, 20154.8.1#

First Amendment to Warrants Issue Agreement between Cellectis S.A. and Kepler Capital Markets SA, dated June 
6, 2013 (English translation)

F-1

333-202205

10.8.1

March 10, 20154.8.2#

Second Amendment to Warrants Issue Agreement between Cellectis S.A. and Kepler Capital Markets SA, dated October 
7, 2013 (English translation)

F-1

333-202205

10.8.2

March 10, 20154.9#

Warrant Agreement between Cellectis S.A. and Trout Capital LLC, dated March 24, 2014

F-1

333-202205

10.9

March 10, 20154.10#

Change of Control Plan, effective as of September 4, 2014 (English translation)

F-1

333-202205

10.10

March 10, 2015




---

ExhibitNumber

Description of Exhibit

Schedule/
Form

File
Number

Exhibit

File Date4.11#

Summary of BSA Plan

F-1

333-202205

10.11

March 10, 20154.12#

Summary of BSPCE Plan

F-1

333-202205

10.12

March 10, 20154.13#

2012 Free Share Plan

F-1

333-202205

10.13

March 10, 20154.14#

2013 Free Share Plan

F-1

333-202205

10.14

March 10, 20154.15#

2014 Free Share Plan

F-1

333-202205

10.15

March 10, 20154.16#

2015 Free Share Plan

20-F

001-36891

4.16

March 21, 20164.17#

2015 Stock Option Plan

20-F

001-36891

4.17

March 21, 20164.18#

2016 Stock Option Plan

S-8

333-214884

99.1

December 2, 20164.19#

2017 Stock Option Plan

S-8

333-222482

99.1

January 9, 20184.20#

Summary of BSA Plan

S-8

333-222482

99.2

January 9, 20184.21#

Free Share 2018 Plan

S-8 POS

333-222482

99.3

April 13, 20184.22#

2018 Stock Option Plan

S-8

333-227717

99.1

October 5, 20184.23#

Summary of BSA Plan

S-8

333-227717

99.2

October 5, 20184.24#

Second Free Share 2018 Plan

S-8

333-227717

99.3

October 5, 20184.25**

License Agreement Between Allogene Therapeutics, Inc. and Cellectis S.A. dated March 8, 2019







Filed herewith4.26**

License, Development and Commercialization Agreement between Les Laboratoires Servier and Cellectis S.A. dated March 6, 2019







Filed herewith4.27#

Management Services Agreement between Cellectis S.A., Cellectis, Inc. and Calyxt, Inc. dated as of January 1, 2016

20-F

001-36891

4.27

March 12, 20194.28#

Management Services Agreement Amendment dated July 25, 2017 between Cellectis S.A. and Calyxt, Inc.

20-F

001-36891

4.28

March 12, 20194.29#

Separation Agreement dated July 25, 2017 between Cellectis S.A. and Calyxt, Inc.

20-F

001-36891

4.29

March 12, 20194.30#

Stockholders Agreement dated July 25, 2017 between Cellectis S.A. and Calyxt, Inc.

20-F

001-36891

4.30

March 12, 20194.31#

License Agreement dated July 25, 2017 between Cellectis S.A. and Calyxt, Inc.

20-F

001-36891

4.31

March 12, 2019




---

ExhibitNumber

Description of Exhibit

Schedule/
Form

File
Number

Exhibit

File Date8.1#

List of subsidiaries of the registrant

20-F

001-36891

8.1

March 12, 201912.1

Certificate of Principal Executive Officer pursuant to Securities Exchange Act Rules 13a-14(a) and 15d- 14(a) as adopted pursuant to Section 
302 of the Sarbanes-Oxley Act of 2002







Filed herewith12.2

Certification by the Principal Financial Officer pursuant to Securities Exchange Act Rules 13a-14(a) and 15d-14(a) as adopted pursuant
 to Section 302 of the Sarbanes-Oxley Act of 2002







Filed herewith13.1#

Certification by the Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 
906 of the Sarbanes-Oxley Act of 2002

20-F

001-36891

13.1

March 12, 201913.2#

Certification by the Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 
906 of the Sarbanes-Oxley Act of 2002

20-F

001-36891

13.2

March 12, 201915.1#

Consent of Ernst & Young et Autres

20-F

001-36891

15.1

March 12, 2019  
Indicates a management contract or any compensatory plan, contract or arrangement. #
Indicates a document previously filed with the Commission. *
Confidential treatment has been granted with respect to certain portions of this exhibit (indicated by
asterisks). Omitted portions have been filed separately with the Securities and Exchange Commission. **
Portions of this exhibit (indicated by asterisks) have been omitted in accordance with the rules of the
Securities and Exchange Commission.




---

SIGNATURES The registrant hereby certifies that it meets all of the requirements for filing on Form 20-F/A and
that it has duly caused and authorized the undersigned to sign this annual report on its behalf.  CELLECTIS S.A./s/ André ChoulikaBy:

André ChoulikaTitle:

Chairman and Chief Executive Officer
 Date: April 25, 2019