BACKGROUND: Hematopoeitic cell transplantation (HCT) in childhood has been associated with late complications including endocrine, neurocognitive, and cardiopulmonary abnormalities. Little is known about the complications of transplantation in infants. PROCEDURE: Eligible subjects underwent HCT for acute lymphoblastic leukemia (ALL) or acute myelogenous leukemia (AML) at less than 3 years of age. Seventeen out of 33 eligible patients were evaluated, transplanted between 1981-2000. Eleven patients had AML, 11 were female. Preparative regimen included total body irradiation (TBI) for eleven. Age at HCT ranged from 0.58 to 2.97 years, and survival 3.25 to 22.33 years. Patients underwent physical and laboratory evaluation, dual-energy X-ray absorptiometry (DXA) scan, bone age X-ray, neuropsychological, and quality of life (QOL) evaluation. RESULTS: Identified abnormalities included: growth hormone deficiency (59%), hypothyroidism (35%), osteochondromas (24%), decreased bone mineral density (24%), and dyslipidemias (59%). Two patients developed a second malignancy. Neuropsychological testing revealed average intelligence quotient (IQ) with attention deficits and other weaknesses for most patients. There were no overall differences between QOL in these children when compared to population norms. CONCLUSIONS: Of the survivors evaluated, typical late effects seen after radiation exposure are common, yet most subjects were doing well without major ongoing medical issues. Dyslipidemias affect more than half of patients and may be associated with metabolic syndrome, placing patients at increased risk for early cardiovascular disease. Even in this group of patients where the majority was exposed to TBI at a very young age, most are functioning at an average or above-average level.