UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 40-F/A

(Amendment No. 1)

[Check one]

| ̈ | REGISTRATION STATEMENT PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ------------------------------------------------------------------------------------

OR



|x | ANNUAL REPORT PURSUANT TO SECTION 13(a) OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ---------------------------------------------------------------------------------------



|                                            |  |                                 
|------------------------------------------- |  | --------------------------------
|For the fiscal year ended December 31, 2013 |  | Commission File Number 001-35446

NOVADAQ TECHNOLOGIES INC.

(Exact name of Registrant as specified in its charter)

Not applicable

(Translation of Registrants name into English (if applicable))

Ontario

(Province or
other jurisdiction of incorporation or organization)

3845

(Primary Standard Industrial Classification Code Number (if applicable))

Not applicable

(I.R.S.
Employer Identification Number (if applicable))

5090 Explorer Drive, Suite 202, Mississauga, Ontario, Canada L4W 4LS
(905) 629-3822

(Address and telephone number of Registrants principal executive offices)

Copies to:



|                                                                                                                            |  |                                                                                                         
|--------------------------------------------------------------------------------------------------------------------------- |  | --------------------------------------------------------------------------------------------------------
|Jeffrey Singer
Stikeman Elliott LLP 5300
Commerce Court West 199 Bay Street
Toronto, Ontario, Canada M5l 1B9
(416) 869-5656 |  | David S. Rosenthal, Esq.
Dechert LLP 1095 Avenue
of the Americas New York, New York 10036
(212) 698-3500

C T Corporation System

111 Eighth Avenue, 13th Floor, New York, New York 10011

(Name, address (including zip code) and telephone number (including area code)

of agent for service in the United States)

Securities registered or to be registered pursuant to Section 12(b) of the Act



|                            |  |                                     
|--------------------------- |  | ------------------------------------
|Title of Each Class         |  | Name of Exchange on Which Registered
|Common Shares, no par value |  | The NASDAQ Stock Market LLC         

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

For annual reports, indicate by check mark the information filed with this Form:



|                          |  |                                      
|------------------------- |  | -------------------------------------
|x Annual Information Form |  | x Audited Annual Financial Statements



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: The Registrant had 54,894,038 Common Shares outstanding as of December 31, 2013

Indicate by check mark whether the Registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Exchange Act 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 x            No  ̈

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web
site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the Registrant was required to
submit and post such files).

Yes
 ̈            No  ̈









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EXPLANATORY NOTE

This Amendment No. 1 on Form 40-F/A (Amendment No. 1) amends the Annual Report on Form 40-F of Novadaq Technologies Inc. (the
Company) for the year ended December 31, 2013, filed with the Securities and Exchange Commission (SEC) on March 28, 2014 (the Original Annual Report). The only amendment to the Original Annual Report is
set forth under the heading Controls and ProceduresManagements Annual Report on Internal Control over Financial Reporting and Attestation Report of Auditor, which sets forth that (i) management of the Company is
responsible for establishing and maintaining adequate internal controls over financial reporting to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial reports for external purposes in
accordance with International Financial Reporting Standards as issued by the International Accounting Standards Board and (ii) as required by National Instrument 52-109 (Certification of Disclosure in Issuers Annual and Interim Filings)
and the United States Securities Exchange Act of 1934, as amended, the Chief Executive Officer and the Chief Financial Officer have caused the effectiveness of the internal controls over financial reporting to be evaluated using the framework
established in Internal ControlIntegrated Framework, 1992 (COSO Framework) published by The Committee of Sponsoring Organizations of the Treadway Commission (COSO).

Other than as discussed above, all information in the Original Annual Report is unchanged and is not reproduced in this Amendment No. 1. This Amendment
No. 1 does not reflect events occurring after the filing of the Original Annual Report or modify or update the disclosure contained in the Original Annual Report in any way other than as discussed above. Accordingly, this Amendment No. 1
should be read in conjunction with the Original Annual Report.

In addition, as required by Rule 12b-15 under the Securities Exchange Act of 1934, as
amended (the Exchange Act), new certifications by the Companys principal executive officer and principal financial officer are filed herewith as Exhibits 99.1 to 99.4 to this Amendment No. 1.

CONTROLS AND PROCEDURES

Managements Annual Report on Internal Control over Financial Reporting and Attestation Report of Auditor

Management is responsible for establishing and maintaining adequate internal controls over financial reporting to provide reasonable assurance regarding the
reliability of financial reporting and the preparation of financial reports for external purposes in accordance with International Financial Reporting Standards as issued by the International Accounting Standards Board. As required by National
Instrument 52-109 (Certification of Disclosure in Issuers Annual and Interim Filings) and the United States Securities Exchange Act of 1934, as amended, the Chief Executive Officer and the Chief Financial Officer have caused the effectiveness
of the internal controls over financial reporting to be evaluated using the framework established in Internal ControlIntegrated Framework, 1992 (COSO Framework) published by The Committee of Sponsoring Organizations of the Treadway
Commission (COSO).The Chief Executive Officer and the Chief Financial Officer of the Company have designed such internal control over financial reporting, or caused it to be designed under their supervision, to provide reasonable assurance regarding
the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with International Financial Reporting Standards as issued by the International Accounting Standards Board, rules of the
Securities Act (Ontario) and the Canadian Securities Authority as at December 31, 2013.

The Company, under the supervision of the Chief Executive
Officer and Chief Financial Officer, has performed control self-assessments as of December 31, 2013 to evaluate the effectiveness of the Companys internal control reporting.

As at December 31, 2013, the Chief Executive Officer and Chief Financial Officer assessed the effectiveness of the Companys internal control over
financial reporting and concluded that such internal control over financial reporting is effective and that there are no materials weaknesses in the Companys internal control over financial reporting that have been identified by management.

In accordance with the United States Jumpstart Our Business Startup Act (the JOBS Act) enacted on April 5, 2012, the Company qualifies
as an emerging growth company (an EGC), which entitles the Company to take



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advantage of certain exemptions from various reporting requirements that are applicable to other public companies that are not EGCs. Specifically, the JOBS Act defers the requirement to have the
Companys independent auditor assess the Companys internal controls over financial reporting under Section 404(b) of the Sarbanes-Oxley Act. As such, the Company is exempted from the requirement to include an auditor attestation
report in this Form 40-F.

UNDERTAKING AND CONSENT TO SERVICE OF PROCESS

A. Undertaking

The Registrant undertakes to make
available, in person or by telephone, representatives to respond to inquiries made by the Commission staff, and to furnish promptly, when requested to do so by the Commission staff, information relating to: the securities registered pursuant to Form
40-F; the securities in relation to which the obligation to file an annual report on Form 40-F arises; or transactions in said securities.

B. Consent
to Service of Process

We have filed a Form F-X in connection with the class of securities in relation to which the obligation to file this report
arises.

Any change in the name or address of the agent for service of process of the Company shall be communicated promptly to the Securities and
Exchange Commission by an amendment to the Form F-X referencing the file number of the registrant.



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SIGNATURES

Pursuant to the requirements of the Exchange Act, the Registrant certifies that it meets all of the requirements for filing on Form 40-F and
has duly caused this annual report to be signed on its behalf by the undersigned, thereunto duly authorized.





NOVADAQ TECHNOLOGIES INC.By:

/s/ Arun MenawatName:

Arun MenawatTitle:

President and Chief Executive Officer




Dated July 17, 2014



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Exhibit Index



|            |  |                                                                                                                      
|----------- |  | ---------------------------------------------------------------------------------------------------------------------
|Exhibit No. |  | Description                                                                                                          
|            | 
|99.1        |  | Certification of Chief Executive Officer pursuant to Rule 13a-14(a) or 15d-14 of the Securities Exchange Act of 1934 
|            | 
|99.2        |  | Certification of Chief Financial Officer required by Rules 13a-14(a) or 15d-14 of the Securities Exchange Act of 1934
|            | 
|99.3        |  | Certification of Chief Executive Officer pursuant to 18 U.S.C. 1350                                                  
|            | 
|99.4        |  | Certification of Chief Financial Officer pursuant to 18 U.S.C. 1350