BackgroundSafe and effective physician-to-physician patient handoffs are integral to patient safety. Unfortunately, poor handoffs continue to be a major cause of medical errors. Developing a better understanding of challenges faced by health care providers is critical to address this continued patient safety threat. This study addresses the gap in the literature exploring broad, cross-specialty trainee perspectives around handoffs and provides a set of trainee-informed recommendations for both training programs and institutions.MethodsUsing a constructivist paradigm, the authors conducted a concurrent/embedded mixed method study to investigate trainees’ experiences with patient handoffs across Stanford University Hospital, a large academic medical center. The authors designed and administered a survey instrument including Likert-style and open-ended questions to solicit information about trainee experiences from multiple specialties. The authors performed a thematic analysis of open-ended responses.Results687/1138 (60.4%) of residents and fellows responded to the survey, representing 46 training programs and over 30 specialties. There was wide variability in handoff content and process, most notably code status not being consistently mentioned a third of the time for patients who were not full code. Supervision and feedback about handoffs were inconsistently provided. Trainees identified multiple health-systems level issues that complicated handoffs and suggested solutions to these threats. Our thematic analysis identified five important aspects of handoffs: (1) handoff elements, (2) health-systems-level factors, (3) impact of the handoff, (4) agency (duty), and (5) blame and shame.ConclusionsHealth systems, interpersonal, and intrapersonal issues affect handoff communication. The authors propose an expanded theoretical framework for effective patient handoffs and provide a set of trainee-informed recommendations for training programs and sponsoring institutions. Cultural and health-systems issues must be prioritized and addressed, as an undercurrent of blame and shame permeates the clinical environment.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12909-023-04355-5.