Sixty patients with reactive arthritis (ReA) and 40 with rheumatoid arthritis (RA), were typed for H LA-B27 and class II antigens DR and DQ, and studied for TAP2 gene polymorphism in comparison with 60 healthy controls. TAP2 polymorphisms at positions 379, 565, 665, and 687 were analyzed using amplification refractory system-based PCR and polymorphisms at positions 386 and 651 using oligonucleotide hybridization. The frequency of the TAP2A/A genotype was 30%(12/40) in RA, in contrast to 13% (8/60) in the controls. This genotype was further associated with DRB1*04 positive RA (10/24, 42%, P=0.01), as well as the TAP2A allele (31/48, 65%, P =0.012). Thr/Thr dimorphism at TAP2 position 665 (24/40, 60%, P=0.024) and Stop/Stop dimorphism at TAP2 position 687 (24/40, 60%, P=0.024) were found to be increased in RA patients as compared to controls. When TAP2I/J polymorphism was studied, TAP2J positivity was found associated with the HLA-B27DR4-DQB1*0301-haplotype in ReA patients. 9/12 of these were positive as compared to 20/60 in random controls (P=0.010). Polymorphisms of the TAP2 gene were found to be associated with subgroups of RA and ReA patients with disease associated markers (e.g. TAP2A in DRB1*04 positive RA, or TAP2J in HLA-B27-DRB1*04-DQB1*0301 positive ReA). These may thus serve as additional markers of specific haplotypes associated with susceptibility to inflammatory arthritis.