Objective: Our purpose was to investigate whether MHC class I and class II antigens, other than B27, were associated with Taiwanese patients with ankylosing spondylitis (AS). Methods: HLA class I and class II antigens were analyzed in B27 positive AS patients (n=130) and B27 positive healthy controls (n=260) using the SSP-DNA typing method. The chi-square test or Fisher's exact test was used to analyze Odds ratio. Results: Allele frequencies of Cw12 (93.85%), Cw7 (20.0%) and Cw8 (9.23%) were found to be significantly increased in AS patients as compared to B27 positive controls (OR 89.09, p<0.0001; OR 6.25, p<0.0001; OR 13.12, p<0.0001, respectively), in which Cw3 (80.0%) was significantly increased (OR 0.12, p<0.0001). Allele frequencies of B75 (6.15%), B60 (20.0%) and B61 (4.62%) were higher in patients (OR 8.46, p=0.003; OR 2.07, p=0.0128; OR 6.24, p=0.0186, respectively), so as higher frequencies of B13 (22.31%) and B58 (36.15%) in controls (OR 0.03, p<0.0001, and OR 0.44, p=0.0011). A11/B27/Cw3 was the most common alleles in controls (70.0%) (OR 0.11, p<0.0001), in contrast to A11/B27/Cw12 in AS patients (78.5%) (OR 21.28, p<0.0001). Furthermore, A33/B58/Cw3 was commonly found both in patients and controls groups (20.0% and 21.54%, respectively) (OR 0.91, p=0.83). The association explained the high allele frequencies of A11/A33, B27/B58, Cw3/Cw3, DR12/DR13, DR17 in B27 (+) controls (15.38%) (p<0.0001) and A11/A33, B27/B58, Cw3/Cw12, DR12/DR13, DR17 in AS patients (15.4%) (p<0.0001). The power of association between AS and HLA-DR15 and DQ2 were found to be low, although significant (p=0.0411 and p=0.0467, respectively). Conclusions: Alleles of A11/B27/Cw12 was closely associated with HLA-B27-positive AS patients, so as A11/B27/Cw3 in B27-positive controls. Our findings are compatible with the hypothesis that alleles of MHC other than B27 may confer further risk to susceptibility of AS.