Much research into the impact of hematopoietic cell transplantation (HCT) on recipients' symptoms, functioning and health-related quality of life uses diverse patient-reported outcome (PRO) measures. Robust conclusions regarding PROs in HCT patients are constrained by methodological issues, including the use of multiple different and noncomparable assessment measures. We reviewed 114 publications addressing PROs in HCT patients. Although three multi-item measures were most frequently used (FACT-BMT, n = 28; European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-C30, n = 26; and SF-36, n = 26), 25 additional measures were used in more than one study. Another 50 measures were used in single studies. Over 50% of studies used more than one measure. We recommend that the field agrees upon a set of measures to address the core domains important to patients, to reduce heterogeneity and allow comparisons across studies and between different populations. Measures should be available in a free and easily accessible manner internationally. We discuss the relative benefits of the National Institutes of Health-supported Patient-Reported Outcomes Measurement Information System (PROMIS) system to achieve these goals. To further address these issues, the Blood and Marrow Transplant Clinical Trials Network has recently created a task force to implement PROMIS measures alongside traditional PRO measures in future clinical trials. Robust comparisons between measures in this setting may allow for the development of a standard for HCT patients.