Jefferies 2016 Healthcare Conference

June 8, 2016

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Safe Harbor

This presentation contains forward looking statements which are made pursuant to the safe harbor provisions of Section 27Aof the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended. Thesestatements are subject to risks and uncertainties which may cause our plans to change or actual results to differ materiallyfrom those anticipated. In particular, unforeseen events outside of our control may adversely impact future results. Additionalinformation concerning these factors is discussed in our reports filed with the Securities and Exchange Commission includingrecent Form 8-Ks, our most recent Annual Report on Form 10K and our most recent Quarterly report on Form 10Q. Theforward looking statements in this presentation reflect management’s current views and may become obsolete as a result ofnew information, future events or otherwise. We may not update such forward looking statements to reflect a change ofevents or circumstances that occur after the date hereof, except as required by law. The industry and market data contained inthis presentation are based on management’s own estimates, independent publications, government publications, reports bymarket research firms or other published independent sources, and, in each case, are believed by management to bereasonable estimates. Although we believe these sources are reliable, we have not independently verified the information.

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Leading Innovator in Bioprocessing

• Repligen is a “pure-play” innovator and manufacturer of high-value products that enable efficiencies in the production of biologics

• The Repligen brand represents:– Best-in-class technology to address modern bioproduction needs

– A premium customer experience: service, quality and technical expertise

• We are building our business through:– Organic growth – Strategic acquisitions – New product innovation and product line extensions– Strength of the biologics commercial market and clinical pipeline

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Strong Execution in 2016 year-to-date

• Renewed key long-term supply agreements for core Protein A ligands business

• Executed on strategic acquisition of Atoll GmBH on April 1 to broaden our fast-growing pre-packed chromatography line

• Raised $111M through convertible bond offering in May

• Recorded Q1 product revenue of $25.1M, up 21% year-over-year

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What Makes Repligen Unique?

Leader in Protein A

Most of the world’s monoclonal antibodies (mAbs) are purified on Protein A ligands manufactured by Repligen

Expanding global presenceMultiple manufacturing sites, 190 employees

Bioprocessing expertise and focus20 of the top biopharmaceutical companies use Repligen products

Chromatography

Filtration Systems

Protein A Ligands

Balanced, diversified portfolio

Cell Culture

Technology and market leadership

Revenue: $83.5M in 2015

“Customer first”Custom solutions

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Strong Revenue Growth & Diversification

Expanding Product Revenue and Gross Profit Margin

DownstreamChromatography

Upstream

Cell CultureUpstreamFiltration

DownstreamProtein A Ligands

DownstreamChromatography

Upstream

Cell Culture DownstreamProtein A Ligands

2012$42M Sales

40% gross margin

2016 guidance $98M-$102M Sales

57%-59% gross margin

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Recent news: Atoll Acquisition

• Acquired Atoll GmBH $9.1 million cash and 538,700 shares of Repligen stock; total upfront = $22.5 million

• Deal includes future contingent payments of €1 million based on defined revenue target for 2016

• Integration expected to be completedby year end 2016

• Expected to add $3.0-$3.5 million in revenue in 2016 (remaining 9 months)

• Expected to be breakeven on adjusted EPS in 2016, accretive in 2017

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Pre-packed leadership and EU base

Repligen Acquires Atoll GmBH- Broadens portfolio, expands customer base and increases capabilities

in growing pre-packed chromatography column market -

WALTHAM, MA – April 4, 2016 – Repligen Corporation (NASDAQ:RGEN), a life sciences company focused on bioprocessing technology leadership, today announced that it has acquired Atoll GmBH (“Atoll”) of Weingarten, Germany, an innovator and manufacturer of MediaScout® pre-packed chromatography columns used in process development and clinical manufacturing of biologic drugs. The acquisition of Atoll expands Repligen’s pre-packed column chromatography portfolio into high throughput process development screening, complementing the Company’s existing strength in clinical production-scale columns. The combined offering will provide bioprocessing customers with breadth and flexibility in choosing column size, chromatography media and packed bed formats.

Expands column portfolio into screening and sample prep (process development)

Leverages our investment in the commercial organization

Expands customer base and provides EU operations center

Increases capabilities in fast-growing segment

The Bioprocessing & Biologics Market

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Global Commercial mAb MarketGl

obal

Rev

enue

, $ B

illio

ns

Monoclonal-based therapeutics are the dominant form of biologic drug

“Mature” mAb sales continue to grow with new indications and drug combinations

*Includes biologics that use a mAb manufacturing process

Chart source: Company 10-Ks, internal tracker

>55 marketed mAbs*

7.9 9.6 10.7 12.5 14.08.2 8.0 8.4 9.2 8.47.8 8.0 8.3

8.5 8.76.5 7.3 7.67.0 7.66.0

6.3 6.8 7.0 7.85.7

6.36.6

6.87.1

0.00.8

1.92.8

3.9

$0.0

$10.0

$20.0

$30.0

$40.0

$50.0

$60.0

$70.0

$80.0

$90.0

$100.0

2011 2012 2013 2014 2015

Other

Cimzia

Yervoy

Actemra

Perjeta

Orencia

Synagis

Simponi

Xolair

Erbitux

Tysabri

Stelara

Soliris

Prolia/Xgeva

Eylea

Herceptin

Avastin

Rituxan

Enbrel

Remicade

Humira

7.9 9.6 10.7 12.5 14.08.2 8.0 8.4 9.2 8.47.8 8.0 8.3

8.5 8.76.5 7.3 7.67.0 7.66.0

6.3 6.8 7.0 7.85.7

6.36.6

6.87.1

0.00.8

1.92.8

3.9

$0.0

$10.0

$20.0

$30.0

$40.0

$50.0

$60.0

$70.0

$80.0

$90.0

$100.0

2011 2012 2013 2014 2015

Other

Cimzia

Yervoy

Actemra

Perjeta

Orencia

Synagis

Simponi

Xolair

Erbitux

Tysabri

Stelara

Soliris

Prolia/Xgeva

Eylea

Herceptin

Avastin

Rituxan

Enbrel

Remicade

Humira

$54.4

$62.1

$71.8

$79.2

$89.0

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1

5

23

2 2

6

9

42

2

1

2

0

1

2

3

4

5

6

7

8

9

10

2008 2009 2010 2011 2012 2013 2014 2015 2016(YTD)

Fusion Proteins

mAbs

mAb Approvals on the Rise

• Robust pipeline to sustain strong mAb market growth

• A record 9 mAbs were approved by U.S. FDA 2015

• 4 mAbs approved by FDA year-to-date in 2016*

• The large majority of mAbs are made using products manufactured by Repligen

Num

ber o

f FDA

app

rova

ls

Chart does not include label expansions* As of April 16, 2016

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Biosimilar programs moving to late stage

Sources: Company websites, ReportsnReports ($10B), GaBi Online ($6B)

No.

bio

simila

r mAb

prog

ram

s

Example only. Not inclusive of all biopharma companies with biosimilar mAb programs

Combined global sales for these 6 mAbs exceeded $50B in 2014

The top targeted biologics are monoclonal antibodies

• Analysts estimate the biosimilars market will reach $5B-$10B by 2020 • 4%-10% of biologic drug sales are expected to be biosimilars by 2020

FiledU.S. Ph. 3 Ph. 3 Ph. 3 Ph. 3

Approved Ph. 3 Ph. 3

Ph, 3 Ph. 3

FiledU.S.

Ph. 3 Ph. 3

Ph. 3 Ph. 3

Ph. 3 Ph. 3

Ph. 3

0

1

2

3

4

5

6

Amgen Pfizer Merck Biogen Novartis

Erbitux

Herceptin

Avastin

Rituxan

Enbrel

Remicade

Humira

Blockbuster “reference” mAbs

with patent expirations 2016-

2020:

Our Bioprocessing Products

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Bioprocessing: An Attractive Market

• Biologics market growing at 8%-10% per year

• Increasing need for more flexible and efficient manufacturing driven by healthcare cost pressures and market globalization

• “Sticky products” with high barriers to entry- Risk and cost to change established biomanufacturing processes

• Future growth independent of the clinical or commercial success of any single drug candidate

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• Market leader in perfusion

• Enables continuous processing

• 2016: single-use launch as alternative to stainless steel,new applications, expansion in Asia

• Up to 200 timesmore potent than insulin

• In multiple commercial processes

• 2016: integration with MilliporeSigma, market seeding

• Market leader in pre-packed columns

• Most flexible in resin choice and size

• Multi-site adoption and expansion into large pharma

• 2016: integration of Atoll (line expansion), new manufacturing suites to decrease lead times

• Cost-effective Protein A resins

• In severalcommercial processes, expanding pipeline of Phase1-3 processes

• 2016: AsiaPacuptake

• Fast, reliable, and reproducible quantitation of leached Protein A, and LONG®R3 IGF-I

Optimizing process efficiency and process economics

Repligen’s “Direct” Product Portfolio*

Upstream Downstream Analytics

*Not shown above are Protein A ligands, which are sold through long term supply agreements

16= Direct-to-customer sales or distributor co-promote = Value add reseller

Dow

nstr

eam

Ups

trea

m

Cell retention

Filtration devicesXCell™ ATF System:

$125-$150M market, share 10%-15%, displacing centrifugation

XCell™ ATF Single-use (2016)New applicationsLT growth 10%-15%

Chromatography

OPUS® pre-packed columns:~$165M clinical market, ~30% penetrated, share >30%

MediaScout™ pre-packed columnsProtein A resins, ELISA Kits

OPUS® process-scale displacing self-packed glass MediaScout™ bench- and pilot scaleLT growth 20%+

Cell culture

Growth FactorsLONG®R3 IGF-1:

$75-$80M market, share ~15%Displacing insulin

Clinical to commercial convert LT growth 10%-15%

Growth DriversProducts Market

$350-$400M resin & ligand marketGlobal leader in ligand manufactureSmaller player in Protein A resins

Protein ANew mAb approvals, market expansion, biosimilarsLT growth 10%+

4 Product Franchises in a $700-$800M Addressable Market

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Expanding Global Presence

Manufacturing Sites• Waltham, MA, USA• Lund, Sweden• Weingarten, Germany

Direct Sales Field Applications and Service Specialists

Distributor

Growth Drivers & Financial Overview

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Organic revenue growth

Margin improvement

Acquisitions

GM: Capacity utilization, yieldsOM: Leverage investments in systems and SG&A

Line extensions10%-15% LT

Same customer base, call pointsUpstream-to-downstream spaceImprove cost and/or operational structure

Bioprocessing Growth Drivers

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Line extensions+24%-29% 201510%-15% L-T

Same customer base, call pointsUp- to-downstream spaceImprovement opportunities

($s in MILLIONS) 2014 2015 2016Guidance*

Long-term goal

Product Revenue $60.4 $83.5 $98-$102 $200-$250 by 2020

Product Revenue Growth 27% 38% 17%-22% 10%-15% organic CAGR

Product Gross Margin 53.6% 57.8% 57%-59% 60% margin

Product Gross Profit $32.4 $48.3

GAAP Income from Operations $10.7 $13.8 $18-$20 20%-25% margin

Non-GAAP Adjusted Income from Operations $10.5 $17.8 $21.5-$23.5

GAAP Net Income $8.2M $9.3M $12-$14

Non-GAAP Adjusted Net Income $7.9M $13.4M $15.5-$17.5

GAAP Earnings Per Share (EPS) diluted $0.25 $0.28 $0.35-$0.41

Non-GAAP Adjusted EPS - diluted $0.24 $0.40 $0.45-$0.51

Financial Snapshot

33.0M shares out (33.5M fully diluted), cash $71M at 3/31/16

2016 Guidance is as of May 5 earnings call. This does NOT include impact of subsequent capital raise, potential additional Refine contingent consideration in range of $2.25M - $3.55M, or potential reversal of $2.0 contingent consideration accrued in Q4 2015

See GAAP to Non-GAAP reconciliation tables in Appendix

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• Many opportunities for growth driven by strength of market for biological drugs

• Brand leadership position; Repligen name represents best-in-class technology, premier customer experience

• Solid internal foundation for growth via infrastructure, innovation, strategic acquisition

• Strong financial position to invest in future growth• Prepared to execute on goal to build a $200-$250

million global company by 2020

Well Positioned for Growth

Contact:Sondra NewmanSr. Director Investor Relations781-419-1881snewman@repligen.com

Appendix:Reconciliation Tables

Line extensions+24%-29% 201510%-15% L-T

Same customer base, call pointsUp- to-downstream spaceImprovement opportunities

Reconciliation Table: Income from OperationsYear ended December 31, 2015

Appendix 1

Line extensions+24%-29% 201510%-15% L-T

Same customer base, call pointsUp- to-downstream spaceImprovement opportunities

Reconciliation Table: Net IncomeYear ended December 31, 2015

Appendix 2

Line extensions+24%-29% 201510%-15% L-T

Same customer base, call pointsUp- to-downstream spaceImprovement opportunities

Reconciliation Table: Net Income per ShareYear ended December 31, 2015

Appendix 3