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SEC Letter

 Danielle M. Lauzon

 617.570.1955
dlauzon@goodwinprocter.com

 Goodwin Procter LLP Counselors at Law

 Exchange
Place Boston, MA 02109

 T: 617.570.1000

 F:
617.523.1231

 August 14, 2014

VIA EDGAR AND FEDERAL EXPRESS

 United States
Securities and Exchange Commission

 Division of Corporation Finance

Mail Stop 4561

 100 F. Street, N.E.

Washington, D.C. 20549

 Attention: Jeffrey P. Riedler

Re:
ProQR Therapeutics B.V.

 Draft Registration Statement on Form F-1

 Submitted July 11, 2014

CIK No. 0001612940

 Dear
Mr. Riedler:

 This letter is being submitted on behalf of ProQR Therapeutics B.V. (the “Company”) in response to the
comments of the staff of the Division of Corporation Finance (the “Staff”) of the U.S. Securities and Exchange Commission (the “Commission”) with respect to the Company’s Confidential Draft Registration
Statement on Form F-1 submitted on July 11, 2014 (the “Confidential Draft Registration Statement”), as set forth in your letter dated August 7, 2014 addressed to Daniel de Boer, Chief Executive Officer of the Company (the
“Comment Letter”). The Company is concurrently filing its Registration Statement on Form F-1 (the “Registration Statement”), which includes changes to reflect responses to the Staff’s comments as well as
updates with respect to the Company’s business and operations.

 For reference purposes, the text of the Comment Letter has been
reproduced herein with responses below each numbered comment. For your convenience, we have italicized the reproduced Staff comments from the Comment Letter. Unless otherwise indicated, page references in the Staff’s comments refer to the
Confidential Draft Registration Statement, and page references in the responses refer to the Registration Statement.

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 The responses provided herein are based upon information provided to Goodwin Procter LLP by
the Company. In addition to submitting this letter via EDGAR, we are sending via Federal Express two (2) copies of each of this letter and the Registration Statement (marked to show changes from the Confidential Draft Registration Statement).

 General

1.
We note that there are a number of additional exhibits that still need to be filed. Please provide these exhibits as promptly as possible. Please note that we may have comments on these materials once they are
provided.

 RESPONSE: The Company acknowledges the Staff’s comment and respectfully advises the Staff that the
majority of the exhibits not filed with the Confidential Draft Registration Statement are being filed with the Registration Statement and that it is supplementally providing the Staff with the form of legal opinion (Exhibit 5.1) to the Registration
Statement on the date hereof. The Company will provide the remaining exhibits as promptly as possible.

2.
Please confirm that the graphics included in your registration statement are the only graphics you will use in your prospectus. If those are not the only graphics, please provide any additional graphics prior to
their use for our review.

 RESPONSE: The Company acknowledges the Staff’s comment and confirms that the graphics
included in the Registration Statement, including the new artwork on the inside cover, are the only graphics the Company currently intends to use in its prospectus. If the Company decides to use any additional graphics in its prospectus, it will
provide any such graphics to the Staff prior to their use for the Staff’s review.

3.
Please supplementally provide us with copies of all written communications, as defined in Rule 405 under the Securities Act, that you, or anyone authorized to do so on your behalf, present to potential investors
in reliance on Section 5(d) of the Securities Act, whether or not they retain copies of the communications. Similarly, please supplementally provide us with any research reports about you that are published or distributed in reliance upon
Section 2(a)(3) of the Securities Act of 1933 added by Section 105(a) of the Jumpstart Our Business Startups Act by any broker or dealer that is participating or will participate in your offering

RESPONSE: The Company respectfully advises the Staff that it is supplementally providing the Staff with a copy of an investor presentation that
was distributed during certain “testing-the-waters” meetings, and will supplementally provide copies of any written communications that the Company, or anyone authorized to do so on the Company’s behalf, uses in reliance on
Section 5(d) of the Securities Act. The Company respectfully advises the Staff that no research

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reports about the Company have been published or distributed in reliance upon Section 2(a)(3) of the Securities Act by any broker or dealer that is participating or will participate in the
offering, and to the extent any such research reports are published or distributed, the Company will supplementally provide them to the Staff.

 Market
and Industry Data and Forecasts, page i

4.
We note your statements on page i and page 43 that neither you nor the underwriters “have independently verified any of the data from third-party sources, nor have you or the underwriters ascertained the
underlying economic or other assumptions relied upon therein” and “unless otherwise noted, internal analysis and estimates may not have been verified by independent sources.” It is not appropriate to directly or indirectly disclaim
liability for information in the registration statement. As such, please revise your disclosure to remove any statements indicating that you have not independently verified third-party information or internal analysis and estimates.

 RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on pages ii and 44 to remove
all statements indicating that the Company has not independently verified third-party information or internal analysis and estimates.

 Prospectus
Summary Overview, page 1

5.
We note that AR-010 has been granted orphan drug designation in the United States and the European Union. Please revise your disclosure in this section to indicate the benefits conveyed by orphan drug designation. In
addition, please clarify that the granting of a request for orphan drug designation does not alter the standard regulatory requirements and process for obtaining marketing approval.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosures on pages 1 and 67 to indicate the benefits conveyed
by orphan drug designation as well as to clarify that granting of a request for orphan drug designation does not alter the standard regulatory requirements and process for obtaining marketing approval.

Development of Our Lead Product Candidate, QR-010, in Cystic Fibrosis, page 1

6.
Please expand your disclosure to define the term “pharmacokinetics” at its first use in the last paragraph of this section.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on page 2 to define the term
“pharmacokinetics.”

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 Development of Our First Non-CF Program, QR-110, in Leber’s Congential…, page 2

7.
Please expand your disclosure to define the following terms at their first use in this section of the prospectus summary.

•

lymphoblastoid cells;

•

ciliation; and

•

cilium length.

 RESPONSE: In response to the Staff’s comment, the Company has revised the
disclosure on page 2 to define each of the terms “lymphoblastoid cells,” “cilia” and “cilium length” at their first use in the prospectus summary.

Risk Associated with Our Business, page 3

8.
Please revise your summary of material risks to disclose your accumulated deficit to date.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on page 3 to disclose the Company’s accumulated
deficit as of June 30, 2014.

 Implications of Being an Emerging Growth Company, page 4

9.
Please expand your disclosure to discuss your status as a foreign private issuer and the exemptions available to you as a foreign private issuer. In this regard, please identify those exemptions which overlap with
the ones available to you as an emerging growth company and to what extent you will continue to enjoy any exemptions as a result of your status as a foreign private issuer once you no longer qualify as an emerging growth company.

 RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on pages 4 and 5 to discuss
the Company’s status as a foreign private issuer and the exemptions available to the Company as a foreign private issuer, as well as to identify the exemptions that overlap with the ones available to the Company as an emerging growth company
and to what extent the Company will continue to enjoy any exemptions as a result of its status as a foreign private issuer once it no longer qualifies as an emerging growth company.

Risk Factors

 Risks Related to Our Capital Needs and
Financial Position

 We will require additional capital to fund our operations and if we fail to…, page 9

10.
Please expand your disclosure in this risk factor to quantify the amount of your cash and cash equivalents.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on page 9 to quantify the amount of the
Company’s cash and cash equivalents as of June 30, 2014.

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 Risks Related to Our Dependence on Third Parties

If third parties on which we depend to conduct our pre-clinical studied or any…, page 16

11.
Please expand your disclosure to describe current Good Manufacturing Practices, or cGMPs, the first time you make reference to them in this section of your prospectus.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on page 16 to describe current Good Manufacturing
Practices, or cGMPs, the first time the Company makes reference to them in this section of the prospectus.

 Risks Related to Our Intellectual Property

 We license patent rights from third-party owners or licensees and if we fail…, page 21

12.
This risk factor appears to cover two separate risks, the risk that you will fail to comply with your obligations in your intellectual property licenses and the risk that owners or licensees do not properly or
successfully obtain, maintain or enforce the patents underlying such licenses. Please revise your disclosure to separate these two risks into their own appropriately titled risk factors.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on page 21 to separate the two risks into the risk
factors titled “We license patent rights from third-party owners or licensees and if we fail to comply with our obligations in our intellectual property licenses, we could lose rights that are fundamental to our business” and “If the
third-parties from whom we license patent rights do not properly or successfully obtain, maintain or enforce the patents underlying such licenses, or if they retain or license to others any competing rights, our competitive position and business
prospects may be adversely affected.”

 We may not be able to protect our intellectual property rights throughout the…, page 24

13.
We note your disclosure that many companies have encountered significant problems in protecting and defending intellectual property rights in foreign jurisdictions and that legal systems of certain countries,
particularly certain developing countries, do not favor the enforcement of patents and other intellectual property protection, particularly those relating to biopharmaceuticals. Please expand your disclosure to identify the foreign countries where
you may have difficulties enforcing your patent rights.

 RESPONSE: In response to the Staff’s comment, the Company
has revised the disclosure on page 24 to identify the foreign countries where it may have difficulties enforcing its patent rights.

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 Risks Related to the Commercialization of Our Product Candidates

We face competition from entities that have developed or may develop…, page 25

14.
Please define the term “statistically significant” at its first use in the second paragraph of this risk factor.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on page 26 to define the term “statistically
significant” at its first use in this risk factor.

 Risks Related to Our Business and Strategy

Our ability to use our net operating losses to offset future taxable income…, page 33

15.
Please expand your disclosure in this risk factor to quantify your tax loss carry-forwards, to describe the limitations on the use of the carry-forwards and when your carry-forwards begin to expire.

 RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on page 33 to quantify the
Company’s tax loss carry-forwards and to describe the limitations on the use of the carry-forwards and when the carry-forwards begin to expire.

Special Note Regarding Forward-Looking Statements and Industry Data, p. 43

16.
Many of the statements in your submission relate to present facts or conditions, rather than to historical facts or future events. In light of this, the second sentence of this section beginning, “All statements
contained in this prospectus, other than statements of historical fact.,” appears to be overly broad. Please narrow your statement accordingly or remove it.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on page 43 to remove this statement.

Management’s Discussion and Analysis of Financial Condition and Results of Operations

Results of Operations

 Research and development costs,
page 53

17.
Please provide a quantitative discussion of the nature of research and development expenses for each period presented.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on pages 54-56 and to provide a quantitative
discussion of the nature of research and development expenses for each period presented.

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 General and administrative costs, page 53

18.
Please revise your disclosure to quantify the amount of change due to each factor.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on pages 55-57 to quantify the amount of change due
to each factor.

 Liquidity and Capital Resources

Contractual Obligations and Commitments

 Commitments,
page 56

19.
Please expand your disclosures to include the amount of the potential future milestone payments.

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on page 60 to include the amount of the potential
future milestone payments.

20.
Please confirm whether the commitments related to the development of QR-010 due in 2014 have been recorded as liabilities in the financial statements.

RESPONSE: The Company acknowledges the Staff’s comment and respectfully advises the Staff that the commitments related to the development
of QR-010 have been recorded as liabilities in the audited financial statements to the extent that the Company had an executed agreement relating to such commitments in place as of December 31, 2013 and activities had been performed under such
agreements as of December 31, 2013. Commitments for which the Company had an executed agreement as of December 31, 2013 but which had not been performed as of December 31, 2013 are not recorded as liabilities in the audited financial
statements, but have been disclosed as commitments in Note 19 to the audited financial statements.

21.
Please expand your disclosure in this section to describe the “commitments related to the development of QR-010 amounting to 953,000 euros, all of which is due in 2014.”

RESPONSE: In response to the Staff’s comment, the Company has revised the disclosure on page 60 to include further explanation of the
nature of the com