The aim of this study was to investigate the association of single nucleotide polymorphisms (SNPs) in tissue non-specific alkaline phosphatase (TNAP) with ankylosing spondylitis (AS) in the Chinese Han population. We carried out both case-control studies in two independent Chinese AS cohorts (Eastern Chinese, Southeastern Chinese) involving 353 AS patients and 514 unrelated healthy controls and family-based association study involving 57 pedigrees. Two TNAP intronic SNPs rs3767155 (G/A), and rs1780329 (G/T) and 1 exonic variant rs3738099 (A/G) were genotyped using direct DNA sequencing method. The results showed that there was no significant difference in allele, genotype or haplotype frequencies between the AS patients and the controls at the three SNPs in either case-control or family-based association study, which indicated that the TNAP gene was unlikely to play a major role in the susceptibility to AS in the Chinese Han population.