Autoantibodies against DFS70/LEDGF, which is also known as an important partner of HIV-1 integrase, are found in 10% of healthy Japanese people, but in only approximately 2% of patients with systemic autoimmune disease (SAD). We wished to characterize the association of HLA class II alleles with the presence of autoantibodies against this molecule. MHC class II genes (DR, DQ, and DP alleles) were analyzed by the polymerase chain reaction-sequence specific primer method in 24 individuals with anti-DFS70 antibodies. The frequencies of HLA-DRB1*0410, -DQB1*0402, and -DPB1*0301 were increased in anti-DFS70 Ab-positive patients, while HLA-DQB1*0302 was decreased compared to Japanese controls. All anti-DFS70 Ab-positive individuals expressed at least one HLA-DQB1 allele with an aspartic acid at residue 57. The immunogenetic background of Japanese individuals with anti-DFS70 antibodies differs from that of patients with SAD. HLA class II genes influence the production of anti-DFS70 antibodies among individuals with various clinical manifestations.