The goal of patient-centered outcomes research (PCOR) is to help patients and those who care for them make informed decisions about healthcare. However, the clinical research enterprise has not involved patients, caregivers, and other non-providers routinely in the process of prioritizing, designing and conducting research in hematopoietic cell transplantation (HCT). To address this need, the National Marrow Donor Program (NMDP)/Be The Match® engaged patients, caregivers, researchers and other key stakeholders in a two-year project with the goal of setting a PCOR agenda for the HCT community. Through a collaborative process, we identified six major areas of interest: 1) Patient, Caregiver and Family Education and Support; 2) Emotional, Cognitive and Social Health; 3) Physical Health and Fatigue; 4) Sexual Health and Relationships; 5) Financial Burden; and 6) Models of Survivorship Care Delivery. We then organized into multi-stakeholder Working Groups to identify gaps in knowledge and make priority recommendations for critical research to fill those gaps. Gaps varied by Working Group, but all noted that a historical lack of consistency in measures utilized and patient populations made it difficult to compare outcomes across studies and urged investigators to incorporate uniform measures and homogenous patient groups in future research. Some groups advised that additional pre-emptory work is needed before conducting prospective interventional trials, whereas others felt ready to proceed with comparative clinical effectiveness research studies. This report presents the results of this major initiative, and makes recommendations by Working Group on priority questions for PCOR in HCT.