Purpose: The aim of our study was to evaluate the impact of genomic polymorphisms of methylene-tetrahydrofolate-reductase (MTHFR) and glutathione S-transferases (GST) on liver toxicities seen in patients receiving busulfan and cyclophoshamide conditioning followed by allogeneic HSCT.Background: Polymorphisms of methylene-tetrahydrofolate-reductase (MTHFR) have been shown to potentially influence toxicity (e.g. mucositis) in HSCT. Additionally, many chemotherapeutics that have been linked to veno-occlusive disease (VOD) and liver toxicity (e.g. Busulfan) are metabolised by glutathione S-transferases (GST). Little is known about the impact of gene polymorphisms of MTHFR and various GSTs on VOD and liver toxicity in allogeneic HSCT.Methods: 84 adult patients were enrolled in this retrospective study. The majority of the patients had chronic myelogenous leukemia (CML) in 1st chronic phase (94%). 2 patients suffered from acute myelogenous leukemia (AML-M4), 2 from myelodysplastic syndrome (MDS) and 1 patients from Farber's disease. DNA was isolated from leucocytes of stem cell recipients collected prior to HSCT. Common gene polymorphisms of glutathione S-transferases (GSTP1-Ile105Val, GSTA1*A/B, GSTM1, GSTT1) and methylene-tetrahydofolate-reductase (MTHFR-C677T, MTHFR-A1298C) were detected by PCR-RFLP. All patients were treated with busulfan/cyclophosphamide as conditioning regimen and received cyclosporine and short-course MTX for GvHD prophylaxis. 67 patients (80%) received additionally anti-thymocyte globulin (ATG). Assessment of liver toxicities was based on appearance of VOD according to the Baltimore criteria, maximum bilirubin levels within 20 days after HSCT and duration of hyperbilirubinaemia > 2 mg/dl.Results: Analyses revealed statistical significant association between the MTHFR-A1298C polymorphism and liver toxicities. There was significant higher incidence of VOD in patients that are homozygous for the C allele (p = 0,04). Independently of VOD, patients carrying the MTHFR-1298CC genotype demonstrated higher median maximum levels of bilirubin with 6.8 mg/dl than MTHFR-1298AC and MTHFR-1298AA patients (3,0 mg/dl and 3,4 mg/dl) (p = 0,004). Furthermore, elevation of bilirubin levels > 2 mg/dl lasted longer in MTHFR-1298CC patients with a median of 14 days compared to 3 and 6 days in patients harbouring the MTHFR-1298AC and MTHFR-1298AA genotype (p = 0,004). Interestingly, the common MTHFR-C677T polymorphism did not reach statistical significance in accordance to liver toxicity in our study population. No significant associations between GSTP1-Ile105Val, GSTA1*A/B, GSTM1 and GSTT1 polymorphisms and liver toxicity were found in this study.Conclusion: Our data suggest that the MTHFR-A1298C polymorphism is associated with VOD and hyperbilirubinaemia in patients treated with busulfan/cyclophosphamide as conditioning regimen followed by allogeneic HSCT. To the best of our knowledge this the first report linking the MTHFR-A1298C polymorphism to liver toxicity in patients receiving allogeneic HSCT.