Ankylosing spondylitis (AS) is a genetically determined disease. Runt-related transcription factor 3 (RUNX3), tumor necrosis factor family member-associated NF-κB activator binding kinase 1 binding protein (TBKBP1), and peroxisome proliferator-activated receptor-gamma coactivator 1 beta (PPARGC1B) have recently been found to be associated with susceptibility to AS in patients of Western European descent. We hypothesize that these three genes may be related to clinical outcomes of Chinese Han AS patients.Blood samples were drawn from 396 HLA-B27-positive Chinese Han AS patients. Clinical indexes were scored for each patient, including the Bath Ankylosing Spondylitis Functional Index (BASFI), Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), and modified Stoke Ankylosing Spondylitis Spine Score (mSASSS), which measure patients' function of daily life and severity of AS. Twelve tagSNPs were selected from these three genes and genotyped. We analyzed the clinical indexes in different genotyped patients to investigate the relationship between severity of AS and different genotypes.The rs11249215 SNP in RUNX3 and the rs7379457 and rs32579 SNPs in PPARGC1B significantly affect the BASFI score in patients. The rs11249215, rs7551188, and rs1395621 SNPs in RUNX3 significantly affect the BASDAI scores. The two selected single nucleotide polymorphisms (SNPs) in TBKBP1 show no relationship with the clinical outcomes. None of the 12 SNPs is related to mSASSS. In conclusion, RUNX3 is related to both the severity of AS and the function of daily life. PPARGC1B is related to the function of daily life.