Aldeyra Therapeutics : Phase 3 TRANQUILITY Trial Run-In Cohort Conference Call Presentation

January 7, 2021

DATA RELEASE

Initial Symptom and Sign Results

From Run-In Cohort of

Phase 3 TRANQUILITY Trial

in Dry Eye Disease

Nasdaq: ALDX

© Aldeyra Therapeutics, Inc. 2021

Disclaimers and Forward-Looking Statements

This presentation and various remarks which may be made during this presentation contain forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995 and Section 21E of the Securities Exchange Act of 1934, as amended, including statements regarding Aldeyra's possible or assumed future results of operations, expenses and financing needs, business strategies and plans, research and development plans or expectations, political, economic, legal, social and health risks, including the recent COVID-19 outbreak and subsequent public health measures and other responses to it, that may affect Aldeyra's business or the global economy, the structure, timing and success of Aldeyra's planned or pending clinical trials, expected milestones, market sizing, pricing and reimbursement, competitive position, regulatory matters, industry environment and potential growth opportunities, among other things. The results of earlier preclinical or clinical trials may not be predictive of future results. As a result of the COVID-19 pandemic, clinical site availability, staffing, and patient recruitment have been negatively affected and the timelines to complete Aldeyra's clinical trials may be delayed. Forward-looking statements include all statements that are not historical facts and, in some cases, can be identified by terms such as "may," "might," "will," "objective," "intend," "should," "could," "can," "would," "expect," "believe," "anticipate," "project," "target," "design," "estimate," "predict," "potential," "plan" or similar expressions and the negatives of those terms.

Forward-looking statements involve known and unknown risks, uncertainties and other factors that may cause Aldeyra's actual results, performance or achievements to be materially different from any future results, performance or achievements expressed or implied by the forward-looking statements. These statements reflect Aldeyra's current views with respect to future events and are based on assumptions and subject to risks and uncertainties, including the development, clinical and regulatory plans or expectations for Aldeyra's product candidates and systems-based approaches, later developments with the FDA that may be inconsistent with Aldeyra's expectations and beliefs, including the risk that the results from smaller clinical trials or portions of clinical trials may not accurately predict results of larger scale trials or the remainder of a clinical trial, inconsistent expectations regarding FDA acceptance and review of the company's filings and submitted data sets, and Aldeyra's continuing review and quality control analysis of clinical data. Important factors that could cause actual results to differ materially from those reflected in Aldeyra's forward-looking statements are described in Aldeyra's most recent Annual Report on Form 10-K and Quarterly Report on Form 10-Q, as well as Aldeyra's subsequent filings with the Securities and Exchange Commission. All of Aldeyra's development plans and timelines may be subject to adjustment depending on funding, recruitment rate, regulatory review, preclinical and clinical results, and other factors any of which could result in changes to Aldeyra's development plans and programs or delay the initiation, completion, or reporting of clinical trials.

In addition to the risks described above and in Aldeyra's other filings with the SEC, other unknown or unpredictable factors also could affect Aldeyra's results. No forward-looking statements can be guaranteed and actual results may differ materially from such statements. The information in this presentation is provided only as of January 7, 2021, and Aldeyra undertakes no obligation to update any forward-looking statements contained in this presentation on account of new information, future events, or otherwise, except as required by law.

2

Initial Results From Run-In Cohort of Phase 3 TRANQUILITY Trial Support First-Line Potential of Reproxalap in Dry Eye Disease

• Statistical significance achieved for both sign and symptoms in dry eye chamber:*
• • Reproxalap demonstrated statistically significant improvement over vehicle in ocular redness (p=0.03), an FDA-approvable objective sign.
  • Reproxalap demonstrated statistically significant improvement over vehicle for the two assessed clinical symptoms: VAS Ocular Dryness (p=0.001) and Ocular Discomfort Score (p<0.0001).
• Acute improvements in ocular symptoms and objective sign within minutes of reproxalap administration in a dry eye chamber.
• 24-hourenvironmental results supportive of reproxalap's rapid and broad efficacy, with consistent directional improvements over vehicle across symptoms and Schirmer's test, and statistical significance vs. vehicle achieved in four of eight assessed outcome measurements.
• The main cohort of TRANQUILITY is expected to begin enrollment in February 2021, following completion of tear RASP analysis from the run-in cohort and confirmation of endpoints and patient numbers.

*Based on Mixed Model Repeated Measures (MMRM p values shown above). Topical ocular reproxalap has been studied in over 1,100
patients thus far with no observed safety concerns; mild instillation site irritation is the most commonly reported adverse event in	VAS = Visual Analog Scale	3
clinical trials. Mixed effect model of repeated measures (MMRM) for change from baseline (Time 0).	RASP = Reactive Aldehyde Species

Source: TRANQUILITY Run-In Cohort initial results

Reproxalap Demonstrated Rapid, Broad, and Durable Symptom Improvement Over 12 Weeks of Chronic Therapy in Prior Trials

RENEW-Part 1 Phase 3 Trial

(Induction-Maintenance Dosing)

Reproxalap demonstrated statistically significant

symptom improvements over vehicle

as early as one week after treatment initiation.

Symptom Treatment Difference‡ (Reproxalap-Vehicle) Over Weeks 2 to 12

0-100 Ocular Symptom Scales			Favors Reproxalap
	p-value
VAS: Ocular Dryness (Co-Primary)	0.0004
VAS: Eye Discomfort	0.0025
VAS: Photophobia	0.0041
VAS: Foreign Body Sensation	0.0035
VAS: Itching	0.0346
VAS: Pain	0.0268
VAS: Burning/Stinging	NS
OSDI (Total)	0.0020
	-20-15-10-5 0	5
0-4 & 0-5 Ocular Symptom Scales
OD4S: Grittiness	0.0025
OD4S: Dryness	0.0134
OD4S: Ocular Discomfort	0.0268
OD4S: Burning	0.0306
OD4S: Stinging	0.0239
CAC Ocular Itching Scale	0.0034
Ocular Discomfort Scale	NS

	-0.8-0.6-0.4-0.2 0.0 0.2
‡Treatment Difference of induction-maintenance dosing, defined as the difference between the changes from baseline for the evaluated
drug vs. vehicle (LS Mean Difference ± 95% CI). Ocular Dryness Score co-primary endpoint assessed in pre-specified patient population
having an OD4S dryness baseline score of ≥ 3 (N=170). Topical ocular reproxalap has been studied in over 1,100 patients with no	VAS = Visual Analog Scale	4
observed safety concerns; mild instillation site irritation is the most commonly reported adverse event in clinical trials.	OD4S = Ocular Discomfort & 4-Symptom
Induction-Maintenance dosing defined as QID dosing (4x daily) for weeks 1-4 followed by BID dosing (2x daily) for weeks 5-12.	CAC = Conjunctival Allergen Challenge
Source: Reproxalap RENEW-Part 1 clinical trial results and TRANQUILITY Run-In Cohort initial results.	MMRM = Mixed Effect Model Repeated Measures

TRANQUILITY Run-In Cohort Evaluated Acute Effects of Reproxalap in Dry Eye Disease Patients

Run-In cohort objective:

• Evaluate efficacy of reproxalap compared to vehicle in dry eye disease after single and multiple doses, and after exposure to a dry eye chamber.
• Power and confirm primary and secondary endpoints for the main cohort of the Phase 3 TRANQUILITY clinical trial.

	Initial Results Available Today
Day 1 (24 hour)	Day 2 (Chamber)
•	Dry Eye Symptoms	•	Dry Eye Symptoms
•	Schirmer's Test	•	Ocular Redness

Assessment Currently In Process

Day 1 - Day 2	Main cohort expected to begin
• Tear RASP Levels	enrollment in February 2021,
following completion of tear RASP

analysis from run-in cohort and confirmation of endpoints and patient numbers.

TRANQUILITY Run-In Cohort Design
	Day 1			Day 2
	Environmental	Controlled Chamber
Groups:	Reproxalap 0.25%	Reproxalap 0.25%
	(N = 12)		(N = 12)
	Vehicle (N = 11)	Vehicle (N = 11)
Dosing:	QID	• One dose 2 min prior
				to chamber entry
				• One dose 45 min after
				chamber entry
Measures:	Dry Eye Symptoms	Dry Eye Symptoms
	Schirmer's Test	Ocular Redness
		Tear RASP Levels
		(assessment in process)

QID = Four times daily	5

Reproxalap Demonstrated Rapid And Broad Improvements After Only One Day of Treatment in TRANQUILITY Run-In Cohort

TRANQUILITY Run-In Cohort Day 1 (24 Hours) Results:*

Dry Eye Assessment (Scale)	Change From Baseline
		P-Value
Reproxalap	Vehicle
After Environmental Dosing
(N = 12)	(N = 11)
VAS Dryness (0-100)	-26	+2	0.003
OD4S: Discomfort (0-5)	-0.7	+0.4	0.003
OD4S: Dryness (0-5)	-1.2	+0.1	0.006
OD4S: Grittiness (0-5)	-1.1	+0.1	0.006
OD4S: Burn (0-5)	-0.1	+0.8	0.07
OD4S: Sting (0-5)	-0.1	+0.4	0.23
Ocular Discomfort Scale (0-4)	-0.7	+0.4	0.07
Schirmer's Test (mm)*	+3.4	+1.3	0.30

*Day 1 Schirmer's Test results based on improvement after a single dose; all other Day 1 assessments performed over 24 hours of QID dosing. Topical ocular reproxalap has been studied in over 1,100 patients thus far with no observed safety concerns; mild instillation site irritation is the most commonly reported adverse event in clinical trials.

Source: TRANQUILITY Run-In Cohort initial results

VAS = Visual Analog Scale

OD4S = Ocular Discomfort & 4-Symptom Questionnaire 6 QID = Four times daily

The Dry Eye Chamber:

A Demanding Real-World Drug Assessment of Dry Eye Disease

• Challenge-modeltrials utilizing a controlled chamber are an FDA accepted design for pivotal endpoints.*
• Dry eye chambers control relative humidity, temperature, airflow, and visual tasking in order to stress the ocular surface.
• • Chambers simulate a "bad day" scenario in the life of a dry eye disease sufferer.
• Trial designs utilizing chambers are able to confirm the utility of drugs with rapid onset of action during an acute ocular surface challenge.

*FDA published "Dry Eye: Developing Drugs for Treatment" draft guidance; December 2020.

7

Reproxalap Demonstrated Acute and Durable Improvements in Ocular Dryness in TRANQUILITY Run-In Dry Eye Chamber

TRANQUILITY Run-In Cohort Day 2 Results:

Ocular Dryness Score (VAS) in Dry Eye Chamber

• Drug effect over vehicle observed upon entry and sustained throughout duration of exposure.
• Therapeutic activity demonstrated after first and second doses, representing near-immediate (within minutes) and statistically significant symptom relief vs. vehicle.
• Consistent and statistically significant improvements over vehicle observed across all symptoms evaluated in the chamber.

Mixed effect model of repeated measures (MMRM) for change from baseline (Time 0). Topical ocular reproxalap has been studied in over 1,100	VAS = Visual Analog Scale
patients thus far with no observed safety concerns; mild instillation site irritation is the most commonly reported adverse event in clinical trials.	MMRM = Mixed Model Repeated Measures	8
Source: TRANQUILITY Run-In Cohort initial results

Reproxalap Demonstrated Acute and Durable Improvements in Ocular Discomfort in TRANQUILITY Run-In Dry Eye Chamber

TRANQUILITY Run-In Cohort Day 2 Results:

Ocular Discomfort Scale (0-4) in Dry Eye Chamber

• Drug effect over vehicle observed upon entry and sustained throughout duration of exposure.
• Therapeutic activity demonstrated after first and second doses, representing near-immediate (within minutes) and statistically significant symptom relief vs. vehicle.
• Consistent and statistically significant improvements over vehicle observed across all symptoms evaluated in the chamber.

Mixed effect model of repeated measures (MMRM) for change from baseline (Time 0). Topical ocular reproxalap has been studied in over 1,100	VAS = Visual Analog Scale
patients thus far with no observed safety concerns; mild instillation site irritation is the most commonly reported adverse event in clinical trials.	MMRM = Mixed Model Repeated Measures	9
Source: TRANQUILITY Run-In Cohort initial results

Reproxalap Demonstrated Acute and Durable Improvements in Ocular Redness in TRANQUILITY Run-In Dry Eye Chamber

TRANQUILITY Run-In Cohort Day 2 Results:

Ocular Redness Score (0-4) in Dry Eye Chamber

• Drug effect over vehicle observed upon entry and sustained throughout duration of exposure.
• Therapeutic activity demonstrated after first and second dose, representing near-immediate (within minutes) and statistically significant objective sign relief vs. vehicle.
• Ocular redness is an FDA-approvable objective sign endpoint for dry eye disease.*

*Currently FDA approved dry eye products have utilized Schirmer's Test,

corneal staining, and conjunctival hyperemia (redness) as objective sign measures.

Mixed effect model of repeated measures (MMRM) for change from baseline (Time 0). Topical ocular reproxalap has been studied in over 1,100 patients thus far with no observed safety concerns; mild instillation site irritation is the most commonly reported adverse event in clinical trials. Source: TRANQUILITY Run-In Cohort initial results

VAS = Visual Analog Scale
MMRM = Mixed Model Repeated Measures	10

Reproxalap Has Demonstrated Consistent Symptom and Sign Results Across Two Chamber Challenge Models in Ocular Surface Diseases

		TRANQUILITY Run-In Cohort	Phase 2 Allergic Conjunctivitis Chamber Trial
		Dry Eye Chamber		Allergen Chamber
Disease	DRYNESS		ITCHING
Symptom

Disease Sign	REDNESS		REDNESS

Topical ocular reproxalap has been studied in over 1,100 patients thus far with no observed safety concerns; mild instillation site irritation is the	VAS = Visual Analog Scale
most commonly reported adverse event in clinical trials.	MMRM = Mixed Model Repeated Measures	11
Source: TRANQUILITY Run-In Cohort initial results; Phase 2 Allergen Chamber clinical trial - reproxalap 0.25% (ClinicalTrials.gov #NCT03709121)

TRANQUILITY Main Cohort Clinical Trial Design

• Main cohort trial design, endpoints, and patient numbers to be confirmed following completion of tear RASP analysis from the run-in cohort.
• TRANQUILITY main cohort design options:

Trial Design Option:		Trial Design Option:	Challenge-Model
	Challenge-Model
		+ Environmental Exposure
	Duration:	Two days		Duration:		Four weeks
	Size:	~200 patients total*		Size:		~200 patients total*
	Primary endpoint:	Objective DED Sign		Primary endpoint:	Objective DED Sign
	Secondary endpoints:	Additional DED Sign		Secondary endpoints:	Additional DED Sign
	Design:	and DED Symptoms				and DED Symptoms
	Multi-center randomized,		Design:		Multi-center randomized,
		double-masked, parallel				double-masked, parallel
		design, vehicle-controlled				design, vehicle-controlled
		clinical trial				clinical trial

Main cohort expected to begin enrollment in February 2021.

*Pending final powering based on final run-in cohort results.

12

Upcoming Expected Reproxalap Development Milestones*

Reproxalap dry eye disease

Phase 3 TRANQUILITY main cohort enrollment initiation February 2021

Reproxalap dry eye disease

Phase 3 TRANQUILITY-2 initiation Q1 2021

Reproxalap allergic conjunctivitis

Phase 3 INVIGORATE study top-line results H1 2021

*The timing of clinical trial initiation and completion depends, in part, on restrictions related to COVID-19, the availability	13
of clinical research facilities and staffing, the ability to recruit patients, and regulatory feedback.