Peak oxygen uptake (VO2peak), a measure of aerobic exercise capacity, predicts mortality and morbidity in healthy and diseased individuals. Our aim was to determine VO2peak years after paediatric allogeneic haematopoietic SCT (HSCT) and to identify associations with baseline patient and donor characteristics, transplantation factors, pulmonary function and self-reported sports activity. In this cross-sectional, population-based study, we measured VO2peak, spirometry and diffusion capacity of the lung (DLCO) 3-10 years post HSCT. Z-scores were calculated by reference values from healthy subjects. Self-reported hours of sports activity were obtained by interview. We included 63 patients (mean age (range) 14.4 (7-24) years). HSCT patients exhibited lower mean VO2peak (-1.42 z-score, 95% confidential interval (-1.7; -1.1)) compared with healthy subjects (P<0.001). Sixteen patients (25%) had VO2peak values <-1.96 z-score. Low VO2peak was associated with reduced forced expiratory volume in 1 s (R(2)=0.11, P=0.009), reduced DLCO/VA (R(2)=0.09, P=0.01) and low physical activity (mean VO2peak z-score inactive group: -2.1 vs most active group: -1.1, P=0.02). No associations between VO2peak and diagnosis, donor type or GvHD were found. Although causes for reduced VO2peak may be multiple, our findings stress the need to focus on physical activity post HSCT to prevent lifestyle diseases and improve quality of life.