OBJECTIVES: Patient preference elicitation methods can increase the patient-centeredness of medical decision making by measuring benefit and value. Patients’ perspectives on treatment benefits and risks can be different from those of regulators and care providers. This study aimed to conduct a comprehensive review and evaluation of methods used to assess patient preferences for different treatments in three therapeutic areas: oncology, immunology, and central nervous system (CNS) diseases. METHODS: A search of electronic databases and grey literature identified published articles on patient preference methods and applications. The methods were critically appraised and the literature review was conducted on patient preference studies on pharmaceutical interventions in oncology, immunology, and CNS. RESULTS: Discrete choice experiments (DCE) and conjoint analysis (CA) were the most commonly used methods for patient preference elicitation. Heterogeneity of patient preferences and sample size were key in determining the choice of method. Among the 30 studies included in the final literature review, safety, efficacy, and convenience (dosing and route of administration) were used most often in patient preference surveys to differentiate between different treatment options. Cost attributes were also included in patient preference studies in oncology and immunology, while quality-of-life related attributes were used in oncology and CNS preference studies. CONCLUSIONS: Quantitative methods to elicit patient preferences such as DCE and multicriteria decision analysis (MCDA) are becoming increasingly acceptable by regulatory and payer bodies as part of benefit-risk assessments and health economic evaluations. Considering patient preferences for efficacy, safety, and convenience can help inform regulators’ and payers’ value judgments, increase the patient-centeredness of decision-making, and differentiate products in competitive markets.