Bone marrow transplantation (BMT) is often complicated by acute graft-versus-host disease (aGVHD). In patients transplanted with an HLA-matched donor the occurrence of this complication is believed to be favoured by disparities at the minor histocompatibility antigens (mHA). However, few of these polymorphic molecules have been identified. We sought to determine whether donor/recipient incompatibility for HPA-1, HPA-2, HPA-3, HPA-5 or CD31 (codon 125) antigens represented a risk factor for aGVHD and genotyped these antigens in 70 bone marrow donors and their HLA-identical recipients. All patients were children who received BMT for haematological malignancies at a single institution according to well-defined therapy protocols. Statistical analysis showed that incompatibility for CD31 (codon 125) was a risk factor for grade II-IV aGVHD in the overall patient population, whereas HPA-3 incompatibility predicted aGVHD occurrence in HLA-A2 patients only. The magnitude of the aGVHD risk was directly related to the number of HPA/CD31 incompatibilities. No correlation was found between non-identity for HPA/CD31 and aGVHD. Since incompatibility but not non-identity for CD31 or HPA-3 was a risk factor for aGVHD, we suggest that allelic variants of these molecules can serve as mHA in BMT recipients from HLA-identical donors.