Precision medicine approaches disease treatment and prevention by taking patients’ individual variability in genes, environment, and lifestyle into account. Although the ideas underlying precision medicine are not new, opportunities for its more widespread use in practice have been enhanced by the development of large-scale databases, new methods for categorizing and representing patients, and computational tools for analyzing large datasets. New research methods may create uncertainty for both healthcare professionals and patients. In such situations, frameworks that address ethical, legal, and social challenges can be instrumental for facilitating trust between patients and providers, but must protect patients while not stifling progress or overburdening healthcare professionals. In this perspective, we outline several ethical, legal, and social issues related to the Precision Medicine Initiative’s proposed changes to current institutions, values, and frameworks. This piece is not an exhaustive overview, but is intended to highlight areas meriting further study and action, so that precision medicine’s goal of facilitating systematic learning and research at the point of care does not overshadow healthcare’s goal of providing care to patients.