Objective Endogenous uveitis is a major cause of visual loss mediated by the immune system. The protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene encodes a lymphoid-specific phosphatase that plays a key role in T-cell receptor (TCR) signaling. Two independent functional missense single nucleotide polymorphisms (SNPs) located within the PTPN22 gene (R263Q and R620W) have been associated with different autoimmune disorders. We aimed to analyze for the first time the influence of these PTPN22 genetic variants on endogenous non-anterior uveitis susceptibility. Methods We performed a case-control study of 217 patients with endogenous non-anterior uveitis and 718 healthy controls from a Spanish population. The PTPN22 polymorphisms (rs33996649 and rs2476601) were genotyped using TaqMan allelic discrimination assays. The allele, genotype, carriers, and allelic combination frequencies were compared between cases and controls with χ2 analysis or Fisher’s exact test. Results Our results showed no influence of the studied SNPs in the global susceptibility analysis (rs33996649: allelic P-value=0.92, odds ratio=0.97, 95% confidence interval=0.54–1.75; rs2476601: allelic P-value=0.86, odds ratio=1.04, 95% confidence interval=0.68–1.59). Similarly, the allelic combination analysis did not provide additional information. Conclusions Our results suggest that the studied polymorphisms of the PTPN22 gene do not play an important role in the pathophysiology of endogenous non-anterior uveitis.