Since 1992, miniaturized pulsatile air-driven ventricular assist devices (VADs), "Berlin Heart," have been used at many institutions (36 cases in North America in 19 different institutions) for pediatric use. Heparin-induced thrombocytopenia (HIT II) is a significant complication rarely reported in the setting of adult VAD support; no similar report exists concerning pediatric VAD support. We report on a 13-month-old, 8.1 kg girl who required LVAD support for cardiogenic shock of unclear etiology. The patient had a history of multiple surgical repairs for correction of complex congenital heart disease consisting of a series of left heart obstructive lesions (Shone's complex). Despite aggressive ventilatory and inotropic support, the patient continued to deteriorate and subsequently required extracorporeal life support. After 7 days of conventional venoarterial extracorporeal membrane oxygenation, a 10 ml Berlin Heart VAD was implanted. After implantation, the patient developed persistent low-grade fever of unclear etiology, gradual thrombocytopenia, and deterioration of renal function. On postimplant day 10, the pump required replacement because of concerns about an inlet valve thrombus; the explanted device demonstrated a nearly occlusive clot not appreciable from external inspection. Simultaneously, HIT II was diagnosed as a result of hematology workup for persistent thrombocytopenia. We discuss the unique challenges posed by HIT II complicating pediatric VAD support and in relation to the heparin coating of the device.