BACKGROUND: Autopsy may confirm clinical diagnoses or identify conditions that were not suspected prior to a patient's death. Previous studies evaluating the utility of autopsy in hematopoietic stem cell transplant (HSCT) recipients yielded conflicting results. METHODS: We conducted a retrospective cohort study of children (<18 years of age) undergoing allogeneic HSCT at Duke University who died of any cause between January 1, 1995 and December 31, 2016. We evaluated associations between patient characteristics and autopsy performance using Chi-square or Fisher's exact tests. We reviewed autopsy reports to determine the concordance between pre-autopsy causes of death and pathological diagnoses identified on autopsy. We classified unexpected diagnoses on autopsy using criteria developed by Goldman et al. We evaluated for temporal changes in the autopsy consent rate and the frequency of unexpected diagnoses on autopsy using Cochran-Armitage tests. RESULTS: During the 22-year study period, 475 patients died and had data available on autopsy performance, and 130 (27%) of these patients underwent autopsy. The autopsy consent rate declined over time (P<0.0001), with autopsies being performed for 40% of deaths in 1995-1999 and 17% of deaths in 2009-2016. White patients were more likely to undergo autopsy than non-white patients (P=0.03). There were no associations between autopsy performance and patient age, sex, HSCT indication, or HSCT donor. Unexpected diagnoses were identified in 31 (24%) autopsies. The proportion of autopsies with an unexpected diagnosis did not change during the study period (P=0.45). However, infectious diagnoses that would have led to a change in management were more frequently identified on autopsies in 1995-2003 than in 2004-2016 (20% vs. 0%; P=0.001). CONCLUSIONS: The autopsy consent rate for pediatric HSCT recipients at our institution declined substantially over the past several decades. The utility of autopsy in this patient population remains high despite a reduction in the identification of unexpected infections.