Allogeneic HSCT recipients are at risk of various complications during post-transplant follow-up. Some patients may refer to an emergency department (ED) for medical attention, but data on ED visits by HSCT recipients are lacking. 1) Assess ED utilization in HSCT recipients and associated risk factors during post-transplant follow-up. 2) Identify subgroups of HSCT patients presenting to the ED. 3) Analyze outcomes and prognostic factors for hospitalization and 30-day mortality after ED visits. 4) Assess mortality hazards following an ED presentation. A retrospective single-center longitudinal analysis including 557 consecutive recipients of allogeneic HSCT at the Medical University of Vienna, Austria, between 01/2010 and 01/2020. Descriptive statistics, event estimates accounting for censored data with competing risks, latent class analysis, and multivariate regression models were used for data analysis. Out of 557 patients (median age at HSCT: 49 [interquartile range: 39-58] years; f:m = 233:324), 137 (25%) presented to our center's ED at least once during post-HSCT follow-up (median individual follow-up: 2.66 [0.72-5.59] years). Cumulative incidence estimates of a first ED visit in the overall cohort were: 19% at two years, 25% at 5 years, and 28% at 10 years from HSCT. These numbers increased to 34%, 41%, and 43% in patients resident in Vienna. Chronic GVHD was the only risk factor showing a statistically significant association with ED presentation in multivariate analysis (HR 2.34, 95% CI 1.63-3.35). Patients presented with various and often multiple symptoms to the ED. We identified three latent patient groups in the ED, mainly characterized by the time from HSCT, chronic GVHD, and documented pulmonary infection. Hospitalization was required in 132/216 (61%) of all analyzed ED visits; in-hospital mortality and 30-day mortality rates were 13% and 7%, respectively. Active acute GVHD, systemic steroids, documented infection, pulmonary infiltrates, and oxygen supplementation were statistically significant predictors of hospitalization; shorter time from HSCT, pulmonary infiltrates, and hemodynamic instability were independent risk factors for 30-day mortality. ED presentation during the last 30 days increased mortality hazards in the overall cohort (HR 4.56, 95% CI 2.68-7.76) after adjustment for relevant confounders. Every fourth patient sought the ED for medical attention at least once during post-HSCT follow-up. Depending on the presence of identified risk factors, a significant proportion of patients may require hospitalization and be at risk for adverse outcomes. Screening for these risk factors and specialist consultation should be part of managing most HSCT patients presenting to the ED.