Autoantibody production is commonly associated with particular HLA class II phenotypes. The aim of the present study was to investigate whether the presence of antiphospholipid (APL) antibodies and other autoantibodies in women with unexplained recurrent miscarriage was associated with particular human leukocyte antigen (HLA)-DR or -DQ alleles or linked epitopes which have previously been reported as being associated with the recurrent miscarriage syndrome or the presence of APL. In a total of 123 Danish and Czech women with recurrent miscarriage, serum was investigated for six different APL antibodies including anticardiolipin (ACL) antibody. Antinuclear antibodies (ANA), anti-zona pellucida antibodies and anti-sperm antibodies were also investigated. The women were HLA-DR and -DQ typed by DNA-based methods. The frequency of HLA-DR phenotypes did not differ significantly between APL antibody positive recurrent miscarriage patients and APL antibody negative recurrent miscarriage patients or healthy controls. Among ACL antibody positive recurrent miscarriage patients, significantly more were positive for the HLA-DR3 phenotype and negative for the HLA-DR2 phenotypes compared with healthy controls (P < 0.05). Among ANA positive recurrent miscarriage women, 55% carried the HLA-DR3 phenotype compared with 28% of ANA negative patients (P < 0.05) and 21% of healthy controls (P < 0.002). In conclusion, among recurrent miscarriage women, the HLA-DR3 phenotypes seem to predispose to formation of ACL antibodies and ANA. The association between APL antibodies and particular HLA alleles and HLA-linked epitopes reported in studies of patients with lupus erythematosus (e.g. HLA-DR7 and -DR4) could not be confirmed in patients with recurrent miscarriage.