Cipher Pharmaceuticals is a specialty pharmaceutical company focused on improving existing drugs. It has generated revenue from its first drug, Lipofen, and expects a second revenue stream from CIP-Tramadol ER. Its pipeline includes CIP-Isotretinoin for severe acne, which if approved, could generate substantial revenue given the large market. Cipher has a strong financial position with no debt and cash reserves to fund its operations and ongoing clinical trials.

1. October 2011

2. Forward-looking Statements
This presentation may contain forward-looking statements within the meaning of certain securities laws, including the “safe
harbour” provisions of the Securities Act (Ontario) and other provincial securities law in Canada. These forward-looking
statements include, among others, statements with respect to our objectives, goals and strategies to achieve those objectives
and goals, as well as statements with respect to our beliefs, plans, objectives, expectations, anticipations, estimates and
intentions. The words “may”, “will”, “could”, “should”, “would”, “suspect”, “outlook”, “believe”, “plan”, “anticipate”, “estimate”,
“expect”, “intend”, “forecast”, “objective” and “continue” (or the negative thereof), and words and expressions of similar import,
are intended to identify forward-looking statements.
By their very nature, forward-looking statements involve inherent risks and uncertainties, both general and specific, which
give rise to the possibility that predictions, forecasts, projections and other forward-looking statements will not be achieved.
Certain material factors or assumptions are applied in making forward-looking statements and actual results may differ
materially from those expressed or implied in such statements. We caution readers not to place undue reliance on these
statements as a number of important factors, many of which are beyond our control, could cause our actual results to differ
materially from the beliefs, plans, objectives, expectations, anticipations, estimates and intentions expressed in such forward-
looking statements. These factors include, but are not limited to, the applicability of patents and proprietary technology;
possible patent litigation; regulatory approval of products in the Company’s pipeline; changes in government regulation or
regulatory approval processes; government and third-party payer reimbursement; dependence on strategic partnerships for
product candidates and technologies, marketing and R&D services; meeting projected drug development timelines and goals;
intensifying competition; rapid technological change in the pharmaceutical industry; anticipated future losses; the ability to
access capital to fund R&D; and the ability to attract and retain key personnel.
We caution that the foregoing list of important factors that may affect future results is not exhaustive. When reviewing our
forward-looking statements, investors and others should carefully consider the foregoing factors and other uncertainties and
potential events. Additional information about factors that may cause actual results to differ materially from expectations, and
about material factors or assumptions applied in making forward-looking statements, may be found in the body of this
presentation, in the “Risk Factors” section of our Annual Information Form, under “Business Risks” and elsewhere in the
Management’s Discussion and Analysis of Operating Results and Financial Position in our most recent annual and quarterly
financial statements and elsewhere in our filings with Canadian securities regulators, except as required by Canadian
securities laws, the Company does not undertake to update any forward-looking statements; such statements speak only as of
the date made. We do not undertake to update any forward-looking statements, whether written or oral, that may be made
from time to time by us or on our behalf; such statements speak only as of the date made. The forward-looking statements
included herein are expressly qualified in their entirety by this cautionary language.
2

3. Cipher Pharmaceuticals (TSX:DND)
54
clinical trials
Commercial-stage 5
specialty pharma
new drug applications
company focused on 4
improving drugs for Distributor partnerships
better results 2
final FDA approvals
2
growing revenue streams
3

4. Pipeline
Market / Phase Phase Regulatory
Indication I/II III approval Commercial
Launched Q4 2007
Lipofen® Hyperlipidemia
(Kowa Pharma)
Moderate to moderately Launched Q3 2011
CIP-Tramadol ER
severe chronic pain (Vertical Pharma)
Launch expected Q4
CIP-Isotretinoin Severe acne
2012 (Ranbaxy Pharma)
4

5. Lipofen® Status Report
• Kowa Pharmaceuticals - U.S. Distributor
• Strong presence in lipid management market
with Lipofen and Livalo (pitavastatin)
• Expanded to 250 reps in the field in 2010
• Lipofen in P2 position on each call
• Patent-protected until 2015
5

6. Thousands
Ja
$50
$100
$150
$200
$250
$300
$350
$400
$0
n-
0
M 9
ar
-0
M 9
ay
-0
9
Ju
l-0
Se 9
p-
0
No 9
v-
09
Ja
n-
1
M 0
ar
-1
M 0
ay
-1
0
Ju
Lipofen® Royalty Growth
l-1
Se 0
p-
1
No 0
Monthly Royalties (US$)
v-
1
Ja 0
n-
1
M 1
ar
-1
M 1
ay
-1
1
Ju
l-1
1
6

7. U.S. Fenofibrate Opportunity
US$2.0 Billion Market
1,800
1,600
1,400
1,200
1,000
Thousands
800
600
400
200
0
4
5
6
7
8
Ja 9
0
1
05
06
07
08
09
10
11
l-0
l-0
l-0
l-0
l-0
l-0
l-1
l-1
n-
n-
n-
n-
n-
n-
n-
Ju
Ju
Ju
Ju
Ju
Ju
Ju
Ju
Ja
Ja
Ja
Ja
Ja
Ja
TRx NRx
Source: IMS Health 7

8. Pipeline
Market / Phase Phase Regulatory
Indication I/II III approval Commercial
Lipofen® Hyperlipidemia Launched Q4 2007
(Kowa Pharma)
CIP- Moderate to moderately Launched Q3 2011
Tramadol ER severe chronic pain (Vertical Pharma)
Launch expected Q4
CIP-Isotretinoin Severe acne
2012 (Ranbaxy Pharma)
8

9. CIP-TRAMADOL ER: Best in Class Profile
Ultram ER® RyzoltTM CIP-Tramadol ER
Time to reach therapeutic
levels (100ng/ml plasma levels)
240 minutes 60 minutes 60 minutes
Food Effect Yes Yes No
Therapeutically Active
Dosages
100 mg Yes No Yes
200 mg Yes Yes Yes
300 mg Yes Yes Yes
Dosage Format Tablets Tablets Capsules
Significant differentiation to drive promotional success
9

10. CIP-TRAMADOL ER: Fast Onset
Concentration Bioequivalence 200 mg multi-dose (fasted)
(ng/mL) Mean Plasma Concentration (0-24 hours) Tramadol N=38
300
200
100 CIP-TRAMADOL ER
ULTRAM ER
4 8 12 16 20 24
Time (hours) 10

11. CIP-TRAMADOL ER: Status Report
U.S. Canada
• Final FDA approval May 2010 • Final TPD approval Sept 2011
• U.S. patent issued Dec 2010 • Patent issued July 2011
• Completed licensing agreement • Completed licensing agreement
with Vertical Pharmaceuticals with Medical Futures
• US$1.5 million upfront, potential for • US$0.3 million upfront, additional
US$5.5 million in pre- and post- cumulative sales milestones
commercial milestones • Double-digit royalty
• Royalty in mid-teens • ~22 reps for launch, plans for
• ~60 reps currently, plans for further expansion
further expansion in H1 2012 • Launching in Q1 2012 as Durela™
• Launched in Q3 2011 as ConZip™
11

12. U.S. Tramadol Opportunity
~US$160 Million Extended-Release Market
Total Tramadol TRx vs. ER TRx
3,500
3,000
2,500
Thousands
2,000
1,500
1,000
500
0
Feb-06 Sep-06 Apr-07 Nov-07 Jun-08 Jan-09 Aug-09 Mar-10 Oct-10 May-11
ER TRx Total Tramadol TRx
Source: IMS Health 12

13. Pipeline
Market / Phase Phase Regulatory
Indication I/II III approval Commercial
Lipofen® Hyperlipidemia Launched Q4 2007
(Kowa Pharma)
CIP- Moderate to moderately severe Launched Q3 2011
Tramadol ER chronic pain (Vertical Pharma)
CIP- Severe acne
Launch expected Q4
Isotretinoin 2012 (Ranbaxy Pharma)
13

14. CIP-ISOTRETINOIN: Opportunity
Best in Class Formulation and First to Market
• Effective treatment requires reaching 120 to 150 mg per kg
over a 5-6 month course of treatment
• Current products have 70% variability in absorption depending
on dietary intake causing inconsistency in getting drug on board
• Demonstrated much greater absorption consistency with or
without food, giving physicians assurance that target
accumulative dose will be achieved regardless of diet
• Expected to be the only promoted isotretinoin product in U.S.
14

15. CIP-ISOTRETINOIN: Profile
Mean Plasma Isotretinoin Conc. AUC: 252.60
(ng/mL)
Phase I: Study No. 2003-627 Cmax: 267.53
Single dose study of Accutane 40mg
Fed vs. Fast Condition
Accutane® 40mg (Fed)
Accutane® 40mg (Fast)
Time (hours) 15

16. CIP-ISOTRETINOIN: Profile
Mean Plasma Isotretinoin Conc. AUC: 106.0
(ng/mL) Phase I: Study No. 2003-627
Cmax: 100.6
Single dose study Accutane 40mg vs.
CIP-Isotretinoin (20mg X 2)
Fed Condition
Accutane® 40mg
CIP-Isotretinoin 2 x 20mg
Time (hours) 16

17. CIP-ISOTRETINOIN: Profile
Mean Plasma Isotretinoin Conc. AUC: 178.8
(ng/mL) Phase I: Study No. 2003-627
Cmax: 200.2
Single dose study Accutane 40mg vs.
CIP-Isotretinoin (20mg X 2)
Fast Condition
CIP-Isotretinoin 2 x 20mg
Accutane® 40mg
Time (hours) 17

18. U.S. Isotretinoin Opportunity
US$0.5 Billion Market (Generic)
Total Isotretinoin Market
140,000
120,000
100,000
80,000
60,000
40,000
20,000
0
Jun-04 Feb-05 Oct-05 Jun-06 Feb-07 Oct-07 Jun-08 Feb-09 Oct-09 Jun-10 Feb-11
Source: IMS Health 18

19. CIP-ISOTRETINOIN: Status Report
Clinical – Phase III Safety Study
• 900+ patients in the U.S. and Canada
• Approved under SPA
• Top-line results released in Q3 2011
• Positive safety data: both drugs showed similar adverse event profiles
• Efficacy data:
• Under PP analysis, both efficacy endpoints met non-inferiority margins
• In mixed LOCF analysis of ITT population, both efficacy endpoints met non-inferiority
margins
• In the LOCF analysis of the ITT population, the first primary endpoint was achieved while
the second fell slightly outside non-inferiority target
Regulatory/Commercial
• FDA and Health Canada submissions planned for Q4 2011
• Pre-commercial preparation has commenced
19

20. CIP-ISOTRETINOIN: U.S. Distribution
Ranbaxy Pharmaceuticals (owned by Daiichi Sankyo)
• Subsidiary of global pharmaceutical company
• Dermatology sales presence in U.S. isotretinoin market
• Funded majority of Phase III study
• Up to $24M in pre- and post-commercial milestones
• Royalty in the mid-teens on net sales
• P1 detail position in Year 1 and primarily P1 in Years 2 and 3
20

21. What’s Next?
Lipofen® • Continued royalty revenue
• Initial royalty revenue from U.S. agreement
CIP-TRAMADOL ER
• Canadian launch: Q1 2012
• FDA submission: Q4 2011
CIP-ISOTRETINOIN • Health Canada submission: Q4 2011
• Additional $1.0 million milestone payment: Q4 2011
• Canadian commercialization opportunities
New opportunities • Out-license current products in other markets
• Product portfolio expansion
21

22. Growing Portfolio Value
Q3 2011 Q1 2012
U.S. launch Cdn launch
Q4 2011 FDA Q4 2012
Submission U.S. launch
Revenue ($)
Q3 2011
Health Canada Q2 2012 FDA
approval Response
CIP-Isotretinoin
CIP-Tramadol
Lipofen
2011 2012 2013 2014

23. Financial Review
(In 000’s of CDN$ H1 2011 H1 2010 2010 2009
Royalty Revenue 1,114 981 2,067 1,107
Milestone Revenue 287 2,155 3,318 2,072
R&D Expenses 1,125 523 743 956
OG&A Expenses 1,774 1,941 3,895 4,252
Income / (loss) (1,594) 310 172 (2,715)
Income / (loss) per
(0.07) 0.01 0.00 (0.11)
share
Solid financial position
• No debt, cash at June 30, 2011: $8.6 million
• Shares outstanding: Approx 24.2 million (basic), 26 million (fully diluted)
23

24. Summary
• Steady revenue stream from Lipofen®
• ConZip™ / Durela™ provide second royalty
revenue stream
• CIP-ISOTRETINOIN offers significant financial
upside
• Solid financial position
• Strong core management team
24

25. Questions