Background: Patient-reported outcomes (PROs) can play an important role in personalized medicine. PROs can be viewed as an important fundamental tool to measure the extent of disease and the effect of treatment at the individual level, because they reflect the self-reported health state of the patient directly. However, their effective integration in personalized medicine requires addressing certain conceptual and methodological challenges, including instrument development and analytical issues. Objectives: To evaluate methodological issues, such as multiple comparisons, missing data, and modeling approaches, associated with the analysis of data related to PRO and personalized medicine to further our understanding on the role of PRO data in personalized medicine. Discussion: There is a growing recognition of the role of PROs in medical research, but their potential use in customizing healthcare is not widely appreciated. Emerging insights into the genetic basis of PROs could potentially lead to new pathways that may improve patient care. Knowledge of the biologic pathways through which the various genetic predispositions propel people toward negative or away from positive health experiences may ultimately transform healthcare. Understanding and addressing the conceptual and methodological issues in PROs and personalized medicine are expected to enhance the emerging area of personalized medicine and to improve patient care. This article addresses relevant concerns that need to be considered for effective integration of PROs in personalized medicine, with particular reference to conceptual and analytical issues that routinely arise with personalized medicine and PRO data. Some of these issues, including multiplicity problems, handling of missing values and modeling approaches, are common to both areas. It is hoped that this article will help to stimulate further research to advance our understanding of the role of PRO data in personalized medicine. Conclusion: A robust conceptual framework to incorporate PROs into personalized medicine can provide fertile opportunity to bring these two areas even closer and to enhance the way a specific treatment is attuned and delivered to address patient care and patient needs.