Factor H-associated hemolytic uremic syndrome (HUS) is a genetic form of thrombotic microangiopathy characterized by deficient factor H (HF-1) levels/activity and uncontrolled complement activation. The disorder mostly leads to end-stage renal disease and often recurs after kidney transplantation. We previously demonstrated that in a child with HF-1-associated HUS a simultaneous kidney and liver transplantation restored the defective HF-1 with no recurrence of the disease in the transplanted kidney. Here we describe a second childhood case of HF-1-associated HUS treated by combined kidney and liver transplant and complicated by a fatal, primary non-function of the liver graft. Graft hypoperfusion during surgery triggered ischemia/reperfusion changes and complement activation. Conceivably, as a result of defective complement regulatory potential, massive shedding of vascular heparan sulfates was documented in the transplanted liver. This might have impaired the physiological thromboresistance of vascular endothelium ending with widespread microvascular thrombosis and infarction. This case indicates that more fundamental research is needed before combined liver and kidney transplant is considered an option for children with HF-1-associated HUS.