Hepatic dysfunction is common after allogeneic hematopoietic stem cell transplantation (HSCT). The aim of this retrospective study was to determine the risk factors, frequency, and outcome of hepatic complications post-HSCT in children. Two hundred and thirty-seven cases of allogeneic HSCT in children were included. Data on biochemical liver function at start of HSCT, at +1, +3, +6, and +9 months, and at each subsequent yearly follow-up were extracted. Patients were stratified into groups with hepatocellular (none and mild, and moderate to severe) and hepatobiliary (none and present) dysfunction. Statistical analysis included variables such as diagnosis, age, conditioning regimen, and HLA type. Results: One hundred and fifty-six (66%) patients displayed hepatocellular dysfunction post-HSCT. In most cases transient, but 32% had a persistent abnormality three yr post-HSCT. Risk factors were chronic GVHD (OR 4.20, p = 0.003) and donor HLA-A*01 (OR 2.97, p = 0.02). HLA-DQB1*03 decreased the risk (OR 0.35, p = 0.02). Hepatobiliary dysfunction was less frequent (12%) but carried a poor prognosis. aGVHD grade II–IV (OR 2.7, p = 0.02) and long-term TPN (OR 3.25, p = 0.01) increased the risk. Conclusion: GVHD is an important risk factor for liver dysfunction post-HSCT. Specific HLA types may also contribute as a risk factor, while others seem to have a protective effect.