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Securities and Exchange Commission Letter

 November 4, 2008

 Via Edgar
and Facsimile

 Mr. Jim B. Rosenberg

 Senior
Assistant Chief Accountant

 Securities and Exchange Commission

 450 5th Street
N.W.

 Washington, D.C. 20549-1103

Re:
BioMarin Pharmaceutical Inc.

Form 10-Q for the Quarterly Period Ended June 30, 2008

File No. 0-26727

 Dear Mr. Rosenberg:

 We are writing in response to oral comments received from the Staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”), by
teleconference on October 30, 2008 (the “Staff Comments”), with respect to BioMarin Pharmaceutical Inc.’s (the “Company”) Quarterly Report on Form 10-Q for the quarter ended June 30, 2008 (the “Form
10-Q”). These comments are further comments based on the comments originally made by the Commission by letter dated October 7, 2008 (the “Comment Letter”) and the Company’s responses to those comments made by letter dated
October 16, 2008.

 Set forth below are the Company’s responses to the Staff Comments. We have recited the Staff Comments as provided to us on the
teleconference in italicized, bold type and have followed each comment with the Company’s response thereto.

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 Form 10-Q For the quarterly period ended June 30, 2008

1.
We acknowledge your response to our previous comment No. 2. It is evident that you recorded your sales tax adjustment in the second quarter of 2008. Please confirm that
you identified the error in the same quarter or tell us when you identified the error. In addition, you believe that it was immaterial to all periods presented. Please explain your consideration for not recording the corrected entry given the impact
of the error would reverse over time due to depreciation and product sales and presumably would be immaterial to future periods.

 Response

 In response to Staff’s comment, we identified the error related to sales taxes
associated with inventory and property, plant and equipment on May 7, 2008. The specific circumstance that led to the discovery was a meeting between certain members of our accounting department regarding the Company’s chart of accounts.
After completing the analysis set forth in our response to your comment No. 2 in the Comment Letter, we concluded that the misstatement due to the erroneous expense recognition of sales tax related to inventory and fixed assets to be immaterial
for all prior periods and for the projected financial results for the full year ending December 31, 2008, and that revision of the prior period financial statements was not required. As a result of this analysis and our conclusion regarding the
materiality of the error, the Company considered not recording the adjustment. However, after further consideration of the fact that the financial statement misstatement would have carried on each quarter for several years resulting in proposed
adjustments by our auditors, plus in the interest of full disclosure and presenting accurate financial statements going forward, the Company concluded that it was appropriate to correct the error.

2.
We acknowledge your response to our previous comment No. 3. As previously requested, please revise your MD&A to discuss the impact of this adjustment on your results
of operations for the three and six month periods ending June 30, 2008.

 Response

 In response to Staff’s comment, we propose to include the following disclosure in our MD&A for our quarterly report on Form 10-Q for the third
quarter of 2008 to be filed with the SEC by no later than November 10, 2008. The Company believes that it is appropriate to include the revised disclosure for this item and the other proposed revised disclosures in the Form 10-Q for the third
quarter as opposed to filling a 10-Q/A for the second quarter. For the reasons that were articulated in our response to comment No. 1, we chose to correct the sales tax error in the second quarter of 2008 even though our conclusion was that
that amount was immaterial to prior periods, the three and six months ended June 30, 2008 and to the projected results for 2008. Therefore, we believe that filing a 10-Q/A filing would give undue importance to the adjustment and has the
potential for causing overreaction. However, in the interest of providing additional disclosure on a prospective basis, the Company believes that it is appropriate to include the revised disclosures in the Form 10-Q for the third
quarter of 2008. The third quarter 10-Q filing will be made in the next 7 days and, as it is the disclosure for the most recent quarter, investors will be reviewing the MD&A carefully, insuring that the additional disclosure is properly
disseminated to investors.

 We have underlined text that has been specifically added in response to your comment. We believe that this
disclosure provides investors with a full and complete understanding of the impact of this adjustment to our results of operation for the three and six month periods ending June 30, 2008 and for the nine month period ending September 30,
2008.

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 Results of Operations

 Net Income (Loss)

 Our net
income for the three and nine months ended September 30, 2008 was $0.8 million and $6.3 million, respectively, as compared to a net loss of $5.2 million and $18.4 million for the three and nine months ended September 30, 2007,
respectively. Net income for the three and nine months ended September 30, 2008 increased $6.0 million and $24.7 million primarily as a result of the following (in millions):

Three Months Ended
September 30,

Nine Months Ended
September 30,

 Net loss for the period ended 2007

$
(5.2
)

$
(18.4
)

 Increased Naglazyme gross profit

10.2

30.1

 Increased Kuvan gross profit

13.6

29.3

 Increased Aldurazyme gross profit

14.8

39.8

 Increased research and development expense

(8.9
)

(13.3
)

 Increased selling, general and administrative expenses

(9.4
)

(25.3
)

 Increased losses from BioMarin/Genzyme LLC

(9.0
)

(22.9
)

 Decreased collaborative agreement revenues

(0.7
)

(3.4
)

 Absence of Orapred milestone revenue

—

(4.0
)

 Increased Orapred gross profit

0.4

1.1

 Decreased interest income

(4.5
)

(5.4
)

 Sales tax error correction recorded in Q2 2008

—

0.8

 Increased interest expense

—

(2.1
)

 Other, net

(0.5
)

—

 Net income for the period ended 2008

$
0.8

$
6.3

 The increase in Naglazyme gross profit during the third quarter and first nine months of 2008 as
compared to the same periods of 2007 is the result of additional patients initiating Naglazyme therapy, primarily outside of the U.S., as well as the favorable impact of foreign currency exchange rates on Naglazyme sales from customers based outside
of the U.S. The increase in Kuvan gross profit during the third quarter and first nine months of 2008 as compared to the same periods in 2007 is due to the December 2007 marketing approval for Kuvan in the U.S. The increase in Aldurazyme gross
profit during the third quarter and first nine months of 2008 as compared to the same periods of 2007 is the result of the restructuring of the joint venture with Genzyme and is partially offset by increased losses from BioMarin/Genzyme LLC, also
due to the restructuring. The year-to-date decrease in collaborative agreement revenues primarily relates to lower reimbursable Kuvan development expenses. The increase in selling, general and administrative expense was primarily due to the
continued international expansion of Naglazyme and commercialization of Kuvan in the U.S. The increase in research and development expense was primarily due to increases in development expenses for GALNS, a Duchenne Muscular Dystrophy licensed
product, and other early stage programs. See below for additional information related to the primary net loss fluctuations presented above, including details of our operating expense fluctuations.

 The sales tax error correction recorded during the second quarter of 2008 relates to the out of period adjustment to correct inventory and property,
plant and equipment balances for sales taxes associated with purchases made between April 2007 and March 2008 that were erroneously expensed at the time of purchase. The correction of the error, which was discovered in May 2008,

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reduced operating expenses by $1.2 million during the second quarter of 2008, and also increased net income for the period by the same amount. The
adjustment reduced operating expenses for the six months ended June 30, 2008 by $0.8 million and increased net income for the period by the same amount. The adjustment did not affect the consolidated statement of operations for the three months
ended September 30, 2008, and increased net income during the nine months ended September 30, 2008 by $0.8 million. We believe that the adjustment is immaterial to the results of operations for the second quarter of 2008 when considering
the $64.2 million of total revenues and $59.6 million of total operating expenses that contributed to the net income for the second quarter of 2008. For similar reasons, we believe that it is immaterial for the nine months ended September 30,
2008. Further, we determined that the impact of the adjustment was not material to prior periods or to the expected results for the year ending December 31, 2008, and as such the adjustment was recorded in the second quarter of 2008 under the
provisions of Accounting Principles Board Opinion (APB) No. 28, Interim Financial Reporting.

 Note 4: Joint Venture

3.
Please revise your disclosure in note 4 or in the MD&A to explain the business purpose for restructuring the Joint Venture with Genzyme consistent with your response to
our previous comment No. 4A. In this regard, please ensure that you include the concept of sharing in 50% of Genzyme’s inefficiencies and receiving only 50% of the benefit of improving your own efficiencies.

 Response

 In response to Staff’s comment, we intend to include the following disclosure under Note 4 to the consolidated financial statements to be provided in our quarterly report on Form 10-Q for the third quarter of 2008. We propose to
include the disclosure in the Form 10-Q for the third quarter for the reasons noted in response to comment No. 2. Further, the Company notes that this disclosure has substantially been made to the market through the Company’s press release
related to the restructuring transaction issued in January 2008.We have underlined text that has been specifically added in response to your comment.

 (4) JOINT VENTURE

 Effective January 2008, the Company and Genzyme restructured BioMarin/Genzyme LLC.
Under the revised structure, the operational responsibilities for BioMarin and Genzyme did not significantly change, as Genzyme continues to globally market and sell Aldurazyme and BioMarin continues to manufacture Aldurazyme. The restructuring
had two significant business purposes. First, since each party now has full control over its own operational responsibilities, without the need to obtain the approval of the other party, and the parties do not need to review and oversee the
activities of the other, it reduces management’s time and effort and therefore improves overall efficiencies. Second, since each party will realize 100% of the benefit of their own increased

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operational efficiencies, it increases the incentives to identify and implement cost saving measures. Under the previous 50/50 structure, each company
shared 50% of the expense associated with the other’s inefficiencies and only received 50% of the benefit of its own efficiencies. Specifically, the Company will be able to realize the full benefit of any manufacturing cost reductions and
Genzyme will be able to realize the full benefit of any sales and marketing efficiencies.

 As of January 1, 2008, instead of
sharing all costs and profits equally through the 50/50 joint venture, Genzyme records sales of Aldurazyme to third party customers and pays BioMarin a tiered payment ranging from approximately 39.5 to 50% of worldwide net product sales depending on
sales volume, which is recorded by BioMarin as product revenue. The Company recognizes a portion of the royalty as product transfer revenue when product is shipped to Genzyme. The product transfer revenue represents the fixed amount per unit of
Aldurazyme that Genzyme is required to pay if the product remains unsold by Genzyme. The amount of product transfer revenue is deducted from the calculated royalty amount when the product is sold by Genzyme. Certain research and development
activities and intellectual property related to Aldurazyme continues to be managed in the joint venture with the costs shared equally by BioMarin and Genzyme. Pursuant to the terms of the joint venture restructuring, the Company received
distributions of $16.7 million of cash and $26.8 million of inventory from the joint venture in the first quarter of 2008.

4.
Also in your response to our previous comment No. 4A, you indicate your intention to provide in your MD&A an analysis of the impact of your Joint Venture
restructuring on your liquidity. Please revise your MD&A to provide this analysis. In your response, please ensure you address cash inflows and outflows and impact of quarterly payments from Genzyme on your days sales outstanding receivables.

 Response

 In response to Staff’s comment, we intend to include the following disclosure under the “Liquidity and Capital Resources” section of our MD&A in our quarterly report on Form 10-Q for the third quarter of 2008. We
propose to include the disclosure in the Form 10-Q for the third quarter for the reasons similar to those noted in response to comment No. 2. Further, the Company notes that this disclosure has substantially been made to the market through the
Company’s press release related to its results of operations for the quarter ended March 31, 2008 and the investor conference call related thereto. We have underlined text that has been specifically added in response to your comment.

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 Liquidity and Capital Resources

 Cash and Cash Flow

 As of
September 30, 2008, our combined cash, cash equivalents and short-term investments totaled $563.0 million, a decrease of $22.6 million compared to $585.6 million at December 31, 2007. During the nine months ended September 30, 2008,
we financed our operations primarily through net product sales and available cash, cash equivalents and short-term investments and the related interest income earned thereon.

 The decrease in cash, cash equivalents, and short-term investments during the first nine months of 2008 was $22.6 million, which was $4.2 million more
than the net decrease in cash, cash equivalents, and short-term investments during the first nine months of 2007 of $18.4 million, excluding net offering proceeds of $316.4 million. The primary items contributing to the decrease in net cash outflow
in the first nine months of 2008 were as follows (in millions):

 Net decrease in cash and short-term investments for the first nine months of 2007

$
(18.4
)

 Net decrease in operating spend

17.5

 Increased capital asset purchases

(32.0
)

 Increased cash flows from BioMarin/Genzyme LLC

1.2

 Investment in Summit Corporation plc

(5.7
)

 Cash received from settlement of foreign currency forward contracts

1.4

 Increased proceeds from stock option exercises and ESPP

15.2

 Other

(1.8
)

 Net decrease in cash and short-term investments for the first nine months of 2008

$
(22.6
)

 The decreased net operating spend includes increases in cash receipts from net revenues offset by
increases in cash payments made for operating activities, such as research and development and sales and marketing efforts, as discussed in “Results of Operations” above. Increased capital asset purchases include the purchase of our
facility at

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300 Bel Marin Keys Drive, Novato, California. Increased cash flows from BioMarin/Genzym