HSCT is an established treatment option for some children with life-threatening diseases, but complications remain a major cause of morbidity and mortality. This retrospective data analysis addresses the surgical issues of children with HSCT-related complications. Between 2002 and 2008, HSCT was performed in 240 children for leukemias/lymphomas (n=135), solid tumors (n=59), immunodeficiencies (n=20), lipid storage diseases (n=10), autoimmune diseases (n=9), and others (n=7). HSCT-related complications requiring surgery occurred in 24 cases (10%) and most often in the leukemias/lymphomas group (18/24 cases): HC (cystoscopic irrigation, n=7), pulmonary aspergilloses (resection, n=7), bone necroses (core decompression, n=3), GvHD bowel (colostomy/PEG, n=2), ICH (drainage, n=2), bilateral kidney abscess (nephrectomies/renal transplantation, n=1), aspergillosis of the maxillary sinus (decompression, n=1), and post-traumatic wound healing disorder (meshed skin transplantation, n=1). Survival was 50% in the group with surgery and 62% in the group without (p=0.275). Even though this difference was not statistically significant, surgical intervention should be encouraged in all cases to achieve favorable results.