Thrombotic microangiopathy (TMA) is a rare but serious complication of hematopoietic stem cell transplantation (HSCT). The purpose of our study is to estimate the incidence and risk factors of TMA in 93 out of a total of 12369 children (0.8%) receiving HSCT. HHV6 infection was an independent risk factor associated with increased mortality in patients with TMA (Hazard Ratio: 2.86 [1.01, 8.39], p=0.05), and our study conducts a review of the literature with the association of HHV-6 and complement activation. Studies exploring the pathophysiology of TMA and its relationship to HSCT are needed to optimize the outcome of pediatric patients.