Transplantation-associated thrombotic microangiopathy (TA-TMA) is a significant complication of haematopoietic stem cell transplantation. However, it remains controversial which clinical or laboratory markers are of evident risk and prognostic value. From 2006 to 2013, a nested case control study was carried out in our centre to study the risk and prognostic factors of TA-TMA. A total of 654 consecutive patients who underwent allogeneic haematopoietic stem cell transplantation were studied. Twenty-six (4.0%) patients matched the established diagnostic criteria. Subjects with TA-TMA had significantly higher 3-year none relapse mortality compared with those without (65.4% vs 15.4%, P < 0.0001). Grades 2 to 4 aGVHD and cytomegalovirus viremia were independent risk factors, and serum LDH level >500U/L as well as hypertension were early signs of TA-TMA occurrence. Liver dysfunction and significant gastric bleeding were independent risk factors for TA-TMA related mortality. Subjects with either liver dysfunction or significant gastric bleeding had significantly higher 3 year TA-TMA related mortality cumulative incidence than subjects without. These observations lead to the conclusion that allo-HSCT recipients with grades 2 to 4 aGVHD or cytomegalovirus viremia should be monitored for TA-TMA. Liver dysfunction and significant gastric bleeding are prognostic factors for TA-TMA. Copyright © 2016 John Wiley & Sons, Ltd.