35th Annual J.P. Morgan Healthcare Conference

Jean-Jacques BienaiméChairman and Chief Executive Officer

BioMarin Pharmaceutical Inc.

January 9, 2017

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Safe Harbor Statement

This non-confidential presentation contains‘forward-looking statements’about the business prospects of BioMarin Pharmaceutical Inc., including potential future products in different areas of therapeutic research and development. Results may differ materially depending on the progress of BioMarin’s product programs, actions of regulatory authorities, availability of capital, future actions in the pharmaceutical market and developments by competitors, and those factors detailed in BioMarin’s filings with the Securities and Exchange Commission such as 10-Q, 10-K and 8-K reports.

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2017: BioMarin’s 20th Year Anniversary Two Decades of Innovation and Productivity

>$1.1billion

expected product revenue for FY 2016

2,200+global employees

14million

units of product manufactured in 2016

5approved products

3rdyear in a row voted top 10 most innovative Company, according to Forbes

5products in clinicaldevelopment

27congress presentations around the globe in 2016

68global markets served

20thyear of scientific innovation

118abstracts accepted at global medical meetings in 2016

1300%increase in revenues from 2006 to 2016

5years on average from IND to approval for all marketed products

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Five Approved Products and a Robust Clinical Portfolio

Commercialized Products

Brineura TM for CLN2, or Batten Disease

Pegvaliase for Phenylketonuria

Vosoritide for Achondroplasia

BMN 270 for Hemophilia A

BMN 250 for MPS IIIB, or Sanfilippo Type B

PHASE 1 PHASE 2 PHASE 3 BLA/NDA/MAA

Late-stage Development Pipeline

5

5 Years

IND or CTA Filing 5 years

5 Years

3 Years

5 Years

Rapid Product Development Track Record Efficient drug development drives strong returns on R&D investment

Time to Approval from IND/CTA filing 10 years

4 Years*

* If approved on anticipated April 2017 PDUFA date

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$26 $84

$122

$297 $325

$376 $441

$501 $549

$751

2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016E

VimizimNaglazymeKuvanAldurazyme + Other

$290-$320

$340-$360

Demonstrated Track Record of Consistent Revenue Growth

(Revenues in millions)

$890

$1,100 –$1,150

$340-$360

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Existing Global Infrastructure Generates Revenue WorldwideWill support potential new launches of Brineura in 2017 and Pegvaliase in 2018

Global footprint in 4 key regionsrepresenting 68 countries

Vimizimelosulfase alfa

Indication:Morquio A Syndrome (MPS IVA)

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Vimizim FY 2016 Revenue Guidance $340M-$360M

Over 2000 patients identified• New patient identification continues

• Epidemiology suggests 3000 patients WW

1Q14 2Q14 3Q14 4Q14 1Q15 2Q15 3Q15 4Q15 1Q16 2Q16 3Q16 4Q16E

Reve

nues

in m

illio

ns U

SD

$10M

$20M

$30M

1

14

25

$40M

Robust Revenue Trajectory1Q14 Launch through 3Q16

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2010 2011 2012

Patie

nts I

dent

ified

500

1000

1500

8001,000

1,200

2000

2013

Pace of patient identification

1,400

2014 20150

1,650

1,800

$50M

$60M

$70M

5154

65 59

73

107

$80M

$90M$100M$110M

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2016

2,000

$700M market opportunity based on currently identified patients

79-99

Kuvansapropterin dihydrochloride

Indication:Phenylketonuria (PKU)

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Newly Acquired Markets Help Drive 14% Y/Y Revenue GrowthKuvan FY 2016 revenue guidance $340M-$360M

Significant Worldwide Opportunity• ROW territories acquired from Merck

1Q16• EU exclusivity extended through 2024• ROW markets leverage established

infrastructure• Patient growth 15% Y/Y in NorAm

region• Y/Y revenue growth of 14%• Developing market to prepare for

pegvaliase

1Q15 2Q15 3Q15 4Q15

Reve

nues

in m

illio

ns U

SD

$10M

$20M

$30M

$40M

Revenue growth driven by new patients in the US and addition of international markets

$50M

$60M

$70M

50

6064 65

1Q16

77

2Q16

90

$80M

$90M

$100M

17

60

22

68

ROW

NorAM

3Q16

91

20

71

82-102

4Q16E

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5 Products in Clinical Development

Brineura TM (cerliponase alfa) for CLN2, or Batten Disease

Pegvaliase for Phenylketonuria

Vosoritide for Achondroplasia

BMN 270 for Hemophilia A

BMN 250 for MPS IIIB, or Sanfilippo Type B

PHASE 1 PHASE 2 PHASE 3 BLA/NDA/MAA

Development Pipeline

Potential approval of Brineura in 2017 and Pegvaliase in 2018

Brineuracerliponase alfa

BMN 190

Indication:CLN2 Disorder, or Batten Disease

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CLN2 Attributes:

• Patients appear developmentally normal until ~ 3 years old

• Disease characteristics: • seizures• language and motor loss • dementia • blindness and early death

• Estimated prevalence of approximately 1,200 to 1,600 children

• Currently therapy supportive/palliative only

CLN2 disease results in rapid decline of all functions and death by age 10-12 years

(Age in years)

(Clin

ical

sco

re)

Healthy children score 6

Homogenous Natural Clinical Course of Patients with CLN2

Brineura for CLN2 : Our Next Potential Product Launch

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Effectiveness Demonstrated in Pivotal and Extension Studies

3

5

13

2

0 2 4 6 8 10 12 14

-2

-1

0

1

NUMBER OF SUBJECTS

CH

ANG

E IN

SC

OR

E

(15/23) 65% No Clinical Progression; p = 0.0002

87% Responder Rate; p = 0.0002

Change in Motor-Language CLN2 Scores from Baseline to last 300mg dose (>72 weeks)

Change in Motor-Language CLN2 Scores from Baseline compared to Natural History at 48-81 weeks

p <0.0001 Comparison of mean rate of decline to the Natural History rate of decline (2 points/48 weeks)Consistent p value at > 72 weeks

All patients treated for 72 weeks or more

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EU and US Registrations Under Review

Majority of review questions relate to the use of Natural History as a control arm and robustness of a single small study:

• Comparability of scales between Natural History and clinical study

• Comparability of populations between Natural History and clinical study

• Statistical analysis

• Robustness of response given small data set

April 2017 PDUFA Goal Date; Potential US Launch in 2Q17CHMP decision anticipated 3Q17; potential EU launch 4Q17

PegvaliaseBMN 165

Target indication: Phenylketonuria (PKU)

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Based on recent interactions with the FDA: • Phe lowering alone could support a path to approval

• A more recent data cut will be submitted for regulatory review

• BLA now planned 2Q17

Next steps planned for MAA submission in the EU:• Meeting with EU health authorities to determine regulatory path forward

mid-year

PKU Market Opportunity: • Potentially ~ 5,500 of the ~15,500 diagnosed PKU patients in North America

• Potentially ~ 18,000 of the ~31,000 diagnosed PKU patients in our ex-NorAm territories

Pegvaliase: Recent FDA Feedback Solidifies Path ForwardNext steps established on requirements for BLA filing

VosoritideBMN 111

Target indication: Achondroplasia

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Achondroplasia: Most Common form of Dwarfism

Achondroplasia• In addition to short stature, serious medical

complications include: • foramen magnum compression• sleep apnea• bowed legs• permanent sway of the lower back • spinal stenosis• obesity

• Global market opportunity ~24,000 patients, with ~80% ex-US

Children with Achondroplasia Grow an Average of 4cm/year vs. 6cm/year for Average Height Children

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Vosoritide: Return to Normal Growth Rate Observed at 12 months

Strong Phase 2 Results with 15µg/kg/day dose:

• ~50% increase in growth velocity observed

• Generally well tolerated over 12 months of dosing

Phase 3 Study Design and Next Steps:

• Randomized, placebo-controlled 12-month treatment study with subsequent long-term open-label extension

• Ages 5 – 14, consistent with Phase 2 population• Annualized growth velocity as primary endpoint

• International, multi-site study underway to support global registration

• Anticipate 12-18 months to enroll treatment study

Phase 3 study in achondroplasia initiated December 2016

NagluBMN 250

Target indication: MPS IIIB (Sanfilippo Syndrome, Type B)

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About MPS IIIB:• Rapidly progressive pediatric brain disease caused by NAGLU enzyme deficiency

resulting in accumulation of heparan sulfate (HS) in the brain

• Accumulation of HS leads to progressive cognitive decline, loss of developmental milestones, severe hyperactivity, sleep disorders, loss of mobility, and early death

BMN 250 is an Innovative Product for MPS IIIB:• Leveraging Brineura experience, BMN 250 is an enzyme replacement therapy

delivered directly into the CNS via an intracerebroventricular (ICV) access device • ICV allows for drugs to bypass the blood brain barrier

• Delivery of drug into the CSF allows for distribution within the brain

BMN 250 for MPS IIIB (Sanfilippo Syndrome, Type B)

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Near Normalization of Key Marker (HS) and Marker of Downstream Damage (LAMP2) Delivering BMN 250 using ICV

0

50

100ICVIV

Mean ± SEM

[% n

aglu

-/- v

ehic

le]

Vehicle naglu-/- naglu-/-

BMN 250

Total Heparan Sulfate (Brain) ****

***

VehicleWild Type

Significant reductions in HS needed to reduce tissue damage and potentially improve clinical outcome

0

2

4

6ICVIV

LAMP-2 (Brain)

VehicleWild Type

Vehicle naglu-/- naglu-/-

BMN 250[#

foci

x10

0 pe

r 4x

field

]NOTE: LAMP-2 IHC data for ICV vs. IV analyzed separately

****

ICV-administered BMN 250 significantly reduced pathological GAG accumulation in the brain of mice

The equivalent dose of IV-administered BMN 250 did not produce these profound effects in mice

25BioMarin Confidential – For Internal Use Only

BMN 250 Reduces HS levels to Normal Range in CSF of MPS IIIB Patients

Encouraging biomarker results at lowest dose of 30mg, patients have safely escalated to 100mg

Next Steps:• Continued enrollment of study• Update at WORLD meeting in February

Gene TherapyBMN 270

Target indication: Hemophilia A

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BMN 270 News Today: Data from high-dose patients since July 2016 update

• FVIII levels stabilized

• Mean Annualized Bleed Rate declined 91% for patients previously on prophylactic Factor VIII

• All patients off steroids

• ALT levels (liver function) in or around the normal range

Hemophilia A: Significant Unmet Medical NeedPatients experience spontaneous bleeding events even with FVIII replacement therapy*

Limitations of prophylactic and on-demand FVIII replacement therapy:• Peaks and troughs of FVIII that lead to bleeds

• Additional FVIII infusions required for break-through bleeds despite adherence to prophylaxis

• Progression of joint disease leading to pain, decreased mobility and reduced Quality of Life (QoL)

• Careful planning of physical activities around infusion timing to prevent bleeds

• Potential development of inhibitors

• Need for multiple (2-4) FVIII infusions weekly given short half-life (8-16 hours)

*(Fischer, 2011, Haemophilia); (Berntorp, 2014)) 28

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Peaks and Troughs: Primary Limitation of FVIII Replacement

Bleeding Risk, Activity and Factor Levels

Source: Role of New Prolonged Half-Life Clotting Factors in Hemophilia (NHF 2015)

Time (Days)

90

80

70

60

50

40

30

20

10

00 1 2 3 4 5 6 7 8 9 10 11 12

Fact

or L

evel

(%)

Traditional Factor

Blee

ding

Ris

k

LOWER RISK

HIGH RISK

Extended Half-Life Factor

Extended half life factor replacement does not eliminate the wide swings in peaks and troughs that result in bleeding episodes

Weeks

N=

NormalFVIII

Range:50%-150%

BMN 270: FVIII Levels Stabilized and Maintained out to 50 weeksBaseline FVIII activity for all subjects at study start was <1% of normal level

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BMN 270 Effectiveness Maintained out to 50 Weeks

High-doseSubject #

FVIII level (%)at last update

July 6

Most recent week of

observation

FVIII level (%) at most recent

observation*

1 89 50 121

2 219 42 133

3 271 40 222

4 12 41 16

5 133 40 175

6 69 38 77

7 79 34 62

*Data as of Dec. 9

Baseline FVIII activity for all subjects in BMN 270 study was <1% of normal level

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Prior to Treatment with BMN 270 Annualized Bleeding Rate (ABR) and Annualized Number of FVIII Infusions are Significant

Mean ABR for 6 prophylactic subjects in high dose cohort

Mean Annualized Number of FVIII Infusions for 6 prophylactic subjects in high dose cohort

Before BMN 270* Before BMN 270*

16.3 136.7

Mea

n An

nual

ized

num

ber o

f FVI

IIIn

fusio

ns (n

o. o

f FVI

II in

fusio

ns/y

ear)

Mea

n AB

R (n

o. o

f epi

sode

s/ye

ar)

* Obtained from medical records 32

Annualized Bleeding Rate (ABR) and Annualized Number of FVIII Infusions Declines Dramatically with BMN 270 Treatment

After BMN 270** After BMN 270**

91% Reduction 98% Reduction136.7

Mean ABR for 6 prophylactic subjects in high dose cohort

Mean Annualized Number of FVIII Infusions for 6 prophylactic subjects in high dose cohort

1.5 2.9

5 of 6 had no bleeds requiring FVIII use after week 2

5 of 6 had no FVIII infusions after week 2

* Obtained from medical records **Rates after BMN 270 were based on data after week 2 through last follow-up visit

16.3

Mea

n An

nual

ized

num

ber o

f FVI

IIIn

fusio

ns (n

o. o

f FVI

II in

fusio

ns/y

ear)

Mea

n AB

R (n

o. o

f epi

sode

s/ye

ar)

Before BMN 270* Before BMN 270*

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Liver Function Tests (ALT) in or Around Normal Range

High-doseSubject#

ALT (U/L); (ULN = 43 (U/L))

Peak ALT level Last ALT level*Last ALT Level

Status

1 60 15 Normal

2 95 16 Normal

3 82 42 Normal

4 87 33 Normal

5 43 38 Normal

6 81 45 <1.1 ULN

7 66 27 Normal

Since WFH all ALT results have improved and all patients are off steroids

*Data as of Dec. 9 34

BMN 270: Moving to Registration-enabling Study

Next Steps:• Begin potentially registration-enabling Phase 2b in 3Q17• Complete evaluation of lower dose without prophylactic steroids• Commission gene therapy manufacturing facility mid-2017

News Today on High-dose patients:

• FVIII levels stabilized

• Mean Annualized Bleed Rate declined 91% for patients previously on prophylactic Factor VIII

• All patients off steroids

• ALT levels (liver function) in or around the normal range

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Four Pillars of Growth Driving Value

Strong and Growing Base Business: >$1.1B from Existing Products for FY 2016

Two Potential Near-term Launches: Brineura 2017; Pegvaliase 2018

Two Potential $1 Billion Opportunities on the Horizon:Vosoritide for Achondroplasia; BMN 270 for Hemophilia A

Turning the Corner Towards Profitability: 2017 GAAP Loss/

Expect non-GAAP Breakeven or Better in 2017*

For a detailed description about our use of non-GAAP net income, and the methodology used in calculating such measure, please see the discussion under the heading “Non-GAAP Information included with our most recent quarterly earnings press release, which can be found at: http://investors.biomarin.com/2016-10-27-BioMarin-Announces-Third-Quarter-2016-Financial-Results

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THANK YOU