Hematopoietic stem cell transplantation (HSCT) treats disorders affecting patients of all ages. We studied the rate-corrected cardiac QT interval (QTc) in 995 consecutive children and adults undergoing HSCT at the University of Minnesota. We sought to (1) describe QTc before and after HSCT; (2) describe the change in QTc after HSCT; (3) identify factors affecting QTc and its change; and (4) scrutinize an 'at risk' sub-cohort with a long QTc before HSCT. Pre HSCT: 952 (96%) patients had an evaluable electrocardiography (ECG); median QTc was 426 ms and depended upon disease necessitating transplant. Post HSCT: 506 (51%) patients had an evaluable ECG; median QTc was 441 ms. Intrapatient QTc change: 490 (49%) evaluable patients showed median QTc change (pre to post HSCT) of +16 ms (P<0.0001). At risk group: 68 patients were 'at risk' (long pre-HSCT QTc). In some, 'at-risk' status trended toward predictive of post-transplant nonrelapse mortality. QTc interval prolongation is evident in a large, diverse cohort undergoing HSCT at our institution. Prospective studies of this patient population may be warranted, particularly for 'at-risk' patients who demonstrate significant QTc prolongation both pre and post HSCT.