Introduction: In acute myeloid leukemia (AML) patients undergoing allogeneic haematopoietic stem cell transplantation (HSCT), there is uncertainty about the extent of influence nutritional parameters have on clinical outcomes. In this study, we investigated the association between initial body mass index (BMI) and weight loss during HSCT on clinical outcomes in a well-characterised cohort of AML patients. Methods: We analysed data of the Basel stem-cell transplantation registry (‘KMT Kohorte') including all patients with AML undergoing first allogeneic HSCT from January 2003 to January 2014. We used multivariable regression models adjusted for prognostic indicators (European Group for Blood and Marrow Transplantation risk score and cytogenetics). Results: Mortality in the 156 AML patients (46% female, mean age 46 years) over the 10 years of follow-up was 57%. Compared to patients with a baseline BMI (kg/m2) of 20-25, a low BMI <20 was associated with higher long-term mortality (70 vs. 49%, adjusted hazard ratio 1.97, 95% CI 1.04-3.71, p = 0.036). A more pronounced weight loss during HSCT (>7 vs. <2%) was associated with higher risk for bacterial infections (52 vs. 28%, OR 2.8, 95% CI 0.96-8.18, p = 0.059) and fungal infections (48 vs. 23%, OR 3.37, 95% CI 1.11-10.19, p = 0.032), and longer hospital stays (64 vs. 38 days, adjusted mean difference 25.6 days (15.7-35.5), p < 0.001). Conclusion: In patients with AML, low initial BMI and more pronounced weight loss during HSCT are strong prognostic indicators associated with lower survival and worse disease outcomes. Intervention research is needed to investigate whether nutritional therapy can reverse these associations.