Objective To investigate the distribution of antigen processing genes transporter associated with antigen processing (TAP), low molecular weight proteasome (LMP2) and HLA DM in the Shanghai population and to explore the possible role of these genes in the genetic susceptibility to autoimmune diseases IgA nephropathy(IgAN) and multiple sclerosis(MS) Methods Eighty normal Shanghai Chinese, 60 patients with IgAN and 21 patients with MS were randomly selected and genotyped for antigen processing genes (TAP1, TAP2, LMP2, HLA DMA and DMB) using polymerase chain reaction sequence specific oligonucleotide (PCR SSO) and polymerase chain reaction restriction fragment length polymorphism (PCR RFLP) Two locus linkage disequilibrium analysis was performed Results Four TAP1, 6 TAP2, 2 LMP2, 3 DMA and 4 DMB alleles were observed Statistically significant associations were found between TAP1B TAP2A, TAP1B LMP2H and TAP2D HLA DMA *0101 ( Pc <0 01) There was no association between antigen processing genes and either IgAN or MS Conclusion The polymorphisms of antigen processing genes in this Shanghai population are similar to those observed in the other ethnic populations No association was found between IgAN or MS and any antigen processing genes tested in Shanghai population Objective To investigate the distribution of antigen processing genetic transporter associated with antigen processing (TAP), low molecular weight proteasome (LMP2) and HLA DM in the Shanghai population and to explore the possible role of these genes in the genetic susceptibility to autoimmune diseases IgA nephropathy (IgAN) and multiple sclerosis (MS) Methods Eighty normal Shanghai Chinese, 60 patients with IgAN and 21 patients with MS were randomly selected and genotyped for antigen processing genes (TAP1, TAP2, LMP2, HLA DMA and DMB) specific oligonucleotide (PCR SSO) and polymerase chain reaction restriction fragment length polymorphism (PCR RFLP) Two locus linkage disequilibrium analysis was performed Four TAP1, 6 TAP2, 2 LMP2, 3 DMA and 4 DMB alleles were observed Statistically significant associations were found between TAP1B TAP2A, TAP1B LMP2H and TAP2D HLA DMA * 0101 (Pc <0 01) There was no association between antigen processing genes and either IgAN or MS Conclusion The polymorphisms of antigen processing genes in this Shanghai population are similar to those observed in the other ethnic populations No association was found between IgAN or MS and any antigen processing genes tested in Shanghai population