Cytokines, costimulatory and counter-regulatory molecules play important roles in the regulation of inflammatory response, and are good candidates involved in the development of ankylosing spondylitis (AS). This study investigated the genotypic distribution of proinflammatory cytokines and T-cell negative regulator cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) in healthy subjects and AS patients. Genomic DNA was extracted from 143 AS patients and 166 ethnic-matched healthy subjects. Nine polymorphisms within the genes of interleukin-4 (IL-4) (-34T>C, -81A>G, -285C>T and -589T>C), interleukin-6 (IL-6) (-174G>C), interleukin-10 (IL-10) (-592A>C and -819T>C) and CTLA-4 (-318C>T and +49A>G) were examined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Significantly less AS patients carried the CTLA-4 high-expressing -318 T allele (P = 0.040). The CTLA-4 +49A>G genotypes were associated with circulatory levels of the inflammatory marker C-reactive protein (CRP) (P = 0.022). Our study documented the most complete genetic information of Taiwanese AS patients. The observations that CTLA-4 +49A>G genotypes are associated with circulatory CRP levels and significantly less AS subjects carrying CTLA-4 higher-secretor -318 T allele suggest the level and regulation of inflammation in AS subjects may be pre-determined by and associated with CTLA-4 genotypes.