UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C.20549



FORM 10-K/A

(Amendment No.2)



xANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE

SECURITIES EXCHANGE ACT OF 1934



FOR THE FISCAL YEAR ENDED JUNE 30, 2011



OR



oTRANSITION
REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE

SECURITIES EXCHANGE ACT OF 1934

FOR THE TRANSITION PERIOD FROM _____ TO
__________



COMMISSION FILE NO. 333-148471



NANOVIRICIDES, INC.

(Name of Business Issuer in Its Charter)



|NEVADA                                                         | 76-0674577                          
|-------------------------------------------------------------- | ------------------------------------
|(State or other jurisdiction of incorporation or organization) | (I.R.S. Employer Identification No.)



135 WOOD STREET, SUITE 205, WEST HAVEN,
CONNECTICUT 06516

(Address of principal executive offices)



203-937-6137

(Issuer's telephone number, including area
code)



SECURITIES REGISTERED PURSUANT TO SECTION
12(b) OF THE ACT: NONE



SECURITIES REGISTERED PURSUANT TO SECTION
12(g) OF THE ACT:



|COMMON STOCK, PAR VALUE $0.001 PER SHARE | NONE                                  
|---------------------------------------- | --------------------------------------
|                                         |                                       
|(Title of Class)                         | (Name of exchange on which registered)



Indicate by check mark if the registrant
is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.



YesoNox



Indicate by a check mark if the registrant
is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.



YesoNox



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.



YesxNoo















Indicate by checkmark whether the registrant
has submitted electronically and posted on its corporate Website, if any, every Interactive Data File required to be submitted
and posted pursuant to Rule 405 of Regulation S-T (§229.405 of this chapter) during the preceding 12 months ( or for such
shorter period that the registrant was required to submit and post such files.



YesoNox(Not required by smaller reporting companies)



Indicate
by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be
contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference
in Part III of this Form 10-K or any amendment to this Form 10-K.x



Indicate by check mark whether the registrant
is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See definitions of
“large accelerated filer”, “accelerated filer”, or “smaller reporting company in Rule 12b-2 of the
Exchange Act (check one):



|Large accelerated filero | Accelerated filero        
|------------------------ | --------------------------
|Non-accelerated filerx   | Smaller reporting Companyo



Indicate by check mark whether the registrant
is a shell company (as defined in Rule 12b-2 of the Exchange Act.).



YesoNox



As of December 31, 2011, there were 147,316,827 shares of common
stock of the registrant issued and outstanding.



The aggregate market value of the voting
stock held on December 31, 2010 by non-affiliates of the registrant was $132,756,355 based on the closing price of $1.47 per share
as reported on the OTC Bulletin Board on January 31, 2011, the last business day of the registrant's most recently completed fiscal
second quarter (calculated by excluding all shares held by executive officers, directors and holders known to the registrant of
five percent or more of the voting power of the registrant's common stock, without conceding that such persons are "affiliates"
of the registrant for purposes of the federal securities laws).





Explanatory Note: This
Amendment No. 2 on Form 10-K/A amends our Annual Report on Form 10-K for the fiscal year ended June 30, 2011, which was originally
filed with the SEC on October 13, 2011 and subsequently amended on October 20, 2011. The sole purpose of this Amendment No. 2 on
Form 10-K/A is to address certain comments received by the Securities and Exchange Commission regarding our disclosures in Item
9A(T). Controls and Procedures.















Item 9A(T). Controls and Procedures



Evaluation of Disclosure Controls and Procedures.



Evaluation of Disclosure Controls and
Procedures



We maintain disclosure controls and procedures
that are designed to ensure that information required to be disclosed in our Exchange Act reports is recorded, processed, summarized
and reported within the time periods specified in the Securities and Exchange Commission’s rules and forms and that such
information is accumulated and communicated to our management, including our chief executive and chief financial officer, as appropriate,
to allow for timely decisions regarding required disclosure. Disclosure controls and procedures, no matter how well designed and
operated, can provide only reasonable assurance of achieving the desired control objectives, and management is required to apply
its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Management has designed our disclosure
controls and procedures to provide reasonable assurance of achieving the desired control objectives.



As required by Exchange Act Rule 13a-15(b),
we have carried out an evaluation, under the supervision and with the participation of our management, including our principal
executive and principal financial officer, of the effectiveness of the design and operation of our management, including our principal
executive and principal financial officer, of the effectiveness of the design and operation of our disclosure controls and procedures
as of June 30, 2011.



a) Based upon an evaluation of the effectiveness
of disclosure controls and procedures, our Chief Executive Officer ("CEO") and Chief Financial Officer ("CFO")
have concluded that as of the end of the period covered by this Annual Report on Form 10-K, as amended, our disclosure controls
and procedures (as defined in Rules 13a-15(e) or 15d-15(e) under the Exchange Act) were not effective to provide reasonable assurance
that information required to be disclosed in our Exchange Act reports is recorded, processed, summarized and reported within the
time periods specified by the rules and forms of the SEC and is accumulated and communicated to management, including the CEO and
CFO, as appropriate to allow timely decisions regarding required disclosure.



b) Changes in internal control over financial
reporting. Since the Company is not listed on a national exchange or on an automated interdealer quotation system, it is not required
to have an audit committee or independent directors. We consider this to be a material weakness. The Company is in the process
of addressing this issue by establishing an Audit Committee, appointing independent directors with at least one having financial
expertise.



Management’s Report on Internal
Control Over Financial Reporting



Management is responsible for establishing
and maintaining adequate internal control over financial reporting as defined in Rules 13a- 15(f) under the Securities Exchange
Act of 1934, as amended. Internal control over financial reporting is designed to provide reasonable assurance regarding the reliability
of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted
accounting principles in the United States of America (“GAAP”). We recognize that because of its inherent limitations,
internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness
to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree
of compliance with the policies and procedures may deteriorate.



Management conducted an evaluation of the
effectiveness of our internal control over financial reporting as of June 30, 2011. To evaluate the effectiveness of our internal
control over financial reporting, management used the criteria described in Internal Control — Integrated Framework issued
by the Committee of Sponsoring Organizations of the Treadway Commission (“COSO Framework”). Based on its evaluation
under theInternal Control - Evaluation Framework, due to the material weakness described above, management concluded that
our internal control over financial reporting was not effective as of June 30, 2011. A material weakness is a control deficiency,
or combination of control deficiencies, such that there is a reasonable possibility that a material misstatement of the financial
statements will not be prevented or detected on a timely basis by the Board in the normal course of their duties. See,
AUDITOR’S OPINION PARAGRAPH.















Based on its evaluation under the Internal
Control - Evaluation Framework, due to the material weakness described above, management concluded that our internal control over
financial reporting was not effective as of June 30, 2011.



The material weakness relates to a lack
of a functioning audit committee and a lack of outside directors on the Company’s Board. We intend to initiate measures to
remediate the identified material weakness by establishing a formal audit committee and the appointment of additional outside directors,
one or more of whom may be appointed to a fully functioning audit committee.



During the period ended June 30, 2009,
the Company implemented additional segregation of responsibilities and authorizations for initiating, authorizing and recording
transactions. In addition the Company has engaged the services of a financial consultant to assist in reviewing significant transactions
and the Company’s quarterly and annual financial statements.



Changes in Internal Control Over Financial
Reporting



Other than as described above, there were
no material changes in our internal control over financial reporting (as defined in Rule 13a- 15(f) under the Exchange Act) that
occurred as of June 30, 2011, that have materially affected, or are reasonably likely to materially affect, our internal control
over financial reporting.



Attestation Report of the Independent
Registered Public Accounting Firm



This annual report includes an attestation
report of our registered public accounting firm regarding internal control over financial reporting. The final paragraph of the
Auditor’s Report states:



“Also in our opinion, the financial
statements referred to above present fairly, in all material respects, the financial position of the Company as of June 30, 2011
and 2010 and the results of its operations and its cash flows for the fiscal years then ended and for the period from May 12, 2005
(inception) through June 30, 2011 in conformity with accounting principles generally accepted in the United States of America.”















ITEM 15. EXHIBITS







|Exhibit No. |  | Description                                                                                                                                                                                                                                                                        
|----------- |  | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|            |  |                                                                                                                                                                                                                                                                                    
|31.1        |  | Certification of Chief Executive and Interim Chief Financial Officer required by Rule 13a-14(a) or Rule 15d-14(a) under the Securities Exchange Act of 1934, as amended*                                                                                                           
|            |  |                                                                                                                                                                                                                                                                                    
|32.1        |  | Certification of Chief Executive Officer and Interim Chief Financial Officer required by Rule 13a-14(b) or Rule 15d-14(b) under the Securities Exchange Act of 1934, as amended, and 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.*



_____________



*    Filed herewith.





SIGNATURES



Pursuant to the requirements of Section
13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the
undersigned, thereunto duly authorized.



Dated: June 14, 2012



| | NANOVIRICIDES, INC.                                                             
| | --------------------------------------------------------------------------------
| |                                                                                 
| | /s/ Eugene Seymour, MD                                                          
| | Name:  Eugene Seymour, M.D.                                                     
| | Title:  Chief Executive Officer and Interim Chief Financial Officer and Director
| | (Principal Executive and Accounting Officer)                                    
| |                                                                                 
| |                                                                                 
| | /s/ Anil Diwan                                                                  
| | Name:  Anil Diwan                                                               
| | Title:  President and Chairman of the Board of Directors                        



Pursuant to the requirements of the Securities
Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities
and on the dates indicate



|June 14, 2012 |                                                                                  | 
|------------- | -------------------------------------------------------------------------------- | 
|              | /s/ Eugene Seymour, MD                                                           | 
|              | Name:  Eugene Seymour, MD                                                        | 
|              | Title:  Chief Executive Officer and Interim Chief Financial Officer and Director | 
|              | (Principal Executive and Accounting Officer)                                     | 
|              |                                                                                  | 
|June 14, 2012 | /s/ Anil Diwan                                                                   | 
|              | Name:  Anil Diwan                                                                | 
|              | Title: President and Chairman of the Board of Directors                          |