Osteoarthritis (OA) is the most common form of arthritis and the precise etiology of this disease remains unclear. Genetic factors play a considerable role in pathogenesis of OA. Several OA-susceptibility genes have been identified. Recently, a new emerging role of pitx1 transcription factor in OA pathogenesis has been reported. Paired-like homeodomain transcription factor 1 (PITX1) has been implicated in hind limb development of mice and is essential to maintain cartilage function. Because of the different expression in the knee joint between OA and normal people, PITX1 may be involved in etiology and pathogenesis of OA. The present study is to evaluate the association of the PITX1 polymorphism (rs479632) with knee OA in a Chinese Han population. A case-control association study was conducted. The polymorphism was genotyped in 581 patients who had primary symptomatic knee OA with radiographic confirmation and in 570 matched controls. Allelic and genotypic frequencies were compared between patients and control subjects. No significant difference was detected in genotype or allele distribution between knee OA and control groups (all P > 0.05). The association was also negative even after stratification by sex. Furthermore, no association between the SNP genotype and the clinical variables age, sex, body mass index (BMI), and Kellgren/Lawrence (K/L) score was observed in OA patients. The present study suggests that the PITX1 polymorphism (rs479632) is not a risk factor for knee OA susceptibility in the Chinese Han population. Further studies are needed to give a global view of this polymorphism in pathogenesis of OA.