JUNE 17, 2020 INVESTOR CALL

WORLD FEDERATION OF HEMOPHILIA VIRTUAL SUMMIT UPDATE

FIRST-IN-HUMAN FOUR-YEAR FOLLOW-UP STUDY OF

DURABLE THERAPEUTIC EFFICACY AND SAFETY:

AAV GENE THERAPY WITH VALOCTOCOGENE ROXAPARVOVEC FOR SEVERE HAEMOPHILIA A

2

This press release contains forward-looking statements about the business prospects of BioMarin Pharmaceutical Inc., including without limitation, statements about: (i) the development of BioMarin's valoctocogene roxaparvovec program generally, (ii) the impact of valoctocogene roxaparvovec gene therapy for treating patients with severe hemophilia A, (iii) that Factor VIII activity levels over four years supporting reductions in bleed rates and Factor VIII usage, (iv) the inspection of its gene therapy manufacturing facility by the FDA to be completed during the second quarter of 2020, (v) the licensure of its gene therapy manufacturing facility, including the timing of such licensure, and (vi) the potential approval and commercialization of valoctocogene roxaparvovec for the treatment of severe hemophilia A, including timing of such approval decisions.

These forward-looking statements are predictions and involve risks and uncertainties such that actual results may differ materially from these statements. These risks and uncertainties include, among others: results and timing of current and planned preclinical studies and clinical trials of valoctocogene roxaparvovec, including final analysis of the above interim data; any potential adverse events observed in the continuing monitoring of the patients in the Phase 1/2 trial; the content and timing of decisions by the FDA, the European Commission and other regulatory authorities, including the potential impact of the COVID-19 pandemic on the regulatory authorities' abilities to issue such decisions and the timing of such decisions; the content and timing of decisions by local and central ethics committees regarding the clinical trials; BioMarin's ability to successfully manufacture valoctocogene roxaparvovec; and those other risks detailed from time to time under the caption "Risk Factors" and elsewhere in BioMarin’s Securities and Exchange Commission (SEC) filings, including BioMarin's Quarterly Report on Form 10-Q for the quarter ended March 31, 2020, and future filings and reports by BioMarin. BioMarin undertakes no duty or obligation to update any forward-looking statements contained in this press release as a result of new information, future events or changes in its expectations.

BioMarin® is a registered trademark of BioMarin Pharmaceutical Inc.

Safe Harbor Statement

WELCOME AND INTRODUCTION

DR. HANK FUCHS, PRESIDENT, WORLDWIDE R&D, BIOMARIN

PROFESSOR JOHN PASI, PROFESSOR OF HAEMOSTASIS AND THROMBOSIS, BARTS AND THE LONDON SCHOOL OF MEDICINE AND

DENTISTRY; CHIEF INVESTIGATOR, VALOCTOCOGENE ROXAPARVOVEC CLINICAL STUDY

DR. STEVEN PIPE, LAURENCE A. BOXER RESEARCH PROFESSOR OF PEDIATRICS AND COMMUNICABLE DISEASE, AND PROFESSOR

OF PATHOLOGY AT THE UNIVERSITY OF MICHIGAN; PRINCIPAL INVESTIGATOR, VALOCTOCOGENE ROXAPARVOVEC CLINICAL STUDY

4

Valoctocogene Roxaparvovec (AAV5-hFVIII-SQ) Expression Cassette

• Human factor VIII gene (hFVIII) • B-domain-deleted (BDD) with SQ linker region• Codon-optimized

Rangarajan S, et al. N Engl J Med. 2017;377(26):2519-2530.A1AT = alpha-1-anti-trypsin promoter; ApoE = Apolipoprotein E; HCR = hepatic control region

hFVIII-SQ

Leader

Seq.

• Human liver-specific promoter • Synthetic polyadenylation signal (sPA)• Flanked by inverted terminal repeats (ITRs)

5

BMN 270-201 Participant Disposition & Baseline Characteristics

BMN 270-201 Clinicaltrials.gov identifier NCT02576795; EudraCT number 2014-003880-38

Baseline Characteristics N=15

Age in years, mean (SD) 31 (8)

Race, n (%)AsianBlack or African AmericanWhite

2 (13%)1 (7%)

12 (80%)

Treatment before enrollment, n (%)FVIII prophylaxisOn-demand treatment with FVIII

14 (93%)1 (7%)

Proportion with zero bleeds 2 (13%)

Historical annualised bleeding rate, median

Prophylactic therapy (n=14) 6.5

6×1013 cohort (n=6) 16.5

4×1013 cohort (n=6) 8.0

On-demand treatment (n=1) 25

6×1013 cohort (n=1) 25

Previous disease, n (%)Hepatitis BHepatitis C

1 (7%)5 (33%)

15 participants enrolled and dosed in 4 cohorts

1 participant in the 6×1012 vg/kg dose cohort

1 participant in the 2×1013 vg/kg cohort

7 participants in the 6×1013 vg/kg dose cohort

6 participants in the 4×1013 vg/kg dose cohort

6

All Treated Bleeds - Sustained Reduction in Both 6E13 & 4E13 Cohorts

16.5

0 0 0 0

16.3

1.30.2 0.7 1.3

0

2

4

6

8

10

12

14

16

18

Pre-infusion Y1 post Y2 post Y3 post Y4 post

An

nu

alis

ed

Ble

ed R

ate

(AB

R, e

pis

od

es p

er y

ear)

median ABR mean ABR

*The one participant treated with on-demand rFVIII pre-infusion is excluded

8

0 0 0

12.2

0.9 1.2 0.50

2

4

6

8

10

12

14

16

18

Pre-infusion Y1 post Y2 post Y3 post

An

nu

alis

ed

Ble

ed R

ate

(AB

R, e

pis

od

es p

er y

ear)

median ABR mean ABR

4E13 vg/kg dose cohort (n=6)6E13 vg/kg dose cohort (n=6*)

95% reductionin cumulative mean

ABR to 0.8(post- vs. pre-infusion)

No spontaneous bleeds in 5/6 subjects in Year 3All participants remain off prophylaxis

Baseline Year 1 Year 2 Year 3 Year 4

14% 71% 86% 86% 86%

Baseline Year 1 Year 2 Year 3

17% 83% 67% 67%

% Participants Bleed Free (n=7) % Participants Bleed Free (n=6)

No spontaneous bleeds in 6/7 participants in Year 4 All subjects remain off FVIII prophylaxis

93% reductionin cumulative mean

ABR to 0.9(post- vs. pre-infusion)

7

Annualised FVIII Usage - Sustained Reduction For Both 6E13 & 4E13 Cohorts

136.5

0 0 0 0.5

135.6

1.88.8 5.5 4.6

0

20

40

60

80

100

120

140

160

180

Pre-infusion Y1 post Y2 post Y3 post Y4 post

An

nu

alis

ed

FV

III U

sage

(AFU

, in

fusi

on

s p

er y

ear)

median AFU mean AFU

6E13 vg/kg dose cohort (n=6*)

155.8

0 0.5 1.5

142.8

1.6 6.8 8.4

0

20

40

60

80

100

120

140

160

180

Pre-infusion Y1 post Y2 post Y3 post**

An

nu

alis

ed

FV

III U

sage

(AFU

, in

fusi

on

s p

er y

ear)

median AFU mean AFU

4E13 vg/kg dose cohort (n=6)

*The one participant treated with on-demand rFVIII pre-infusion is excluded

Reduction in FVIII Usage Post-administration

Year 1 Year 2 Year 3 Year 4

Mean 99% 94% 96% 97%

Median 100% 100% 100% 99.6%

Reduction in FVIII Usage Post-administration

Year 1 Year 2 Year 3**

Mean 99% 95% 94%

Median 100% 99.7% 99%

96% reduction in mean FVIII usage to 5.4

(post- vs. pre-infusion)

96% reduction in mean FVIII usage to 5.7

(post- vs. pre-infusion)

**Includes prophylactic rFVIII infusion prior to study-related liver biopsy 6

8

Fact

or

FVII

I Act

ivit

y (I

U/d

L; C

hro

mo

gen

ic A

ssay

)

Study Week

N

Chromogenic Assay FVIII Activity - Enduring For Both 6E13 & 4E13 Cohorts

24.2

7.99.9

16.4

6E13 vg/kg

4E13 vg/kg

Mean FVIII activity level

Median FVIII activity level

9

LOESS (LOcally Estimated Scatterplot Smoother) Curves of

FVIII Activity Level Over Time

Chromogenic Assay FVIII Activity For 6E13 & 4E13 CohortsFa

cto

r FV

III A

ctiv

ity

(IU

/dL;

Ch

rom

oge

nic

Ass

ay)

Study Week

10

Haemophilia Severity Relative to Treated Bleeds & FVIII Usage by Participant

Non-haemophilic (>40 IU/dL) Mild (>5-40 IU/dL) Moderate (1-5 IU/dL) ▲<LLOQ (<3 IU/dL for the chromogenic assay)

Annualised Treated Bleed RateCurrent FVIII Range

▲

▲

Chromogenic One-Stage

Annualised FVIII Usage

6E1

3 v

g/k

g

coh

ort

4E1

3 v

g/k

g

coh

ort

1

2

3

4

5

6

7

8

9

10

11

12

13

Participant #*

*Ordered by FVIII level at Week 156 (4E13 cohort) or 208 (6E13 cohort); highest at top

Baseline Week 5 and beyond Baseline Week 5 and beyond

11

50

60

70

80

90

100

0 52 104 156 208

Me

an T

ota

l Sco

re6E13 cohort 4E13 cohort

Haemo-QoL-A Total Score Over Time

WeekN

6E13

4E13

7 7 5 6 5

6 4 6 6

12

• The most common adverse events (AEs) associated with valoctocogene roxaparvovec included:

• Transient infusion-associated reactions and

• Transient, asymptomatic, and mild to moderate ALT elevations with no long-lasting clinical sequelae

• No emergence of delayed adverse drug reactions

• No treatment-related serious adverse event (SAE) in the past year

–2 SAEs in the past year, both unrelated to valoctocogene roxaparvovec

• No new Grade 3 AEs

• No participants withdrew

• No clinical sequelae to corticosteroid use

• No thrombotic events

• No participants developed FVIII inhibitors

Safety and Tolerability Profile of 6E13 and 4E13 Cohorts Remains Favourable

13

• Study 270-201 represents longest duration of clinical experience for a gene therapy in Haemophilia A

• After 4 years for 6E13 vg/kg cohort and 3 years for 4E13 vg/kg cohort

–All study participants in both dose cohorts remain off prophylactic therapy

–Cumulative mean ABRs remain <1 in both dose cohorts

–The only spontaneous bleeds occurred in previously damaged target joints in the two lowest responding participants

• Haemostatic efficacy was maintained at all FVIII levels

• FVIII activity levels showed shallow decline commensurate with the most recent years’ observations

• Improvements in health-related quality of life in the 6E13 vg/kg cohort maintained

• Safety profile of BMN 270 remains favourable and consistent with previously reported data

• Ongoing haemostatic efficacy established for a fourth year, from a single administration of BMN 270, without the requirement for prophylactic therapy, exemplifies the potential for a paradigm shift in the treatment of haemophilia A

Summary - 4-Year Update For First-In-Human Valoctocogene Roxaparvovec Study

THANK YOU