HLA B27 association with seronegative spondarthritis (SSA) has been recognized for over a decade and its association with chronic synovitis in Haemophilia patients has been recently reported. We characterized the HLA B27 subtypes in a cohort of 98 B27 positive individuals with SSA (n = 45), haemophilia with chronic synovitis (n = 21) and normal controls (n = 32), using polymerase chain reaction-based sequence specific primers (PCR-SSP) and reverse line strip (RLS) techniques. The results revealed a significant association for a novel allele B*2714 in SSA along with the previously reported B*2705 allele. We also found a significant association between haemophilia patients with chronic synovitis from India and a hitherto unidentified allele, B*2708.