Background/aim: Juvenile idiopathic arthritis (JIA) is a chronic complex autoimmune disease. Genetic and environmental factors increase the risk of JIA. It is accepted that alterations in immune system pathways play an important role in the pathogenesis of JIA. The aim of the study was to investigate the possible association between immune system regulatory gene polymorphisms and JIA in Turkish patients. Materials and methods: We analyzed eight polymorphisms, TNF-alpha-863 C > A, TNFRII 196 T > G, IL2-631 G > A, IL13-1112 C > T, CCR2 190 G > A, CCR5delta32, CTLA4-1661 A > G, and PTPN22 1858 C > T, in 76 patients with JIA and in 80 healthy controls, who were of a similar age and same sex. Genotyping was identified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Results: We found significant differences in the genotype frequencies of TNF-alpha-863 C >A variation between the patients and healthy controls (P = 0.007). TNF-alpha-863 C/C wild type genotype was significantly increased risk factor for JIA (OR = 2.56; 95% Cl = 1.30-5.03). Moreover, our results showed that TNFRII 196 T/T genotype frequency was significantly higher in JIA patients compared to controls (P = 0.03; OR = 2.12; 95% Cl = 1.09-4.10). However, we did not find a statistically significant relationship between other polymorphisms and JIA (P > 0.05). Conclusion: These results indicate that TNF-alpha-863 C > A and TNFRII 196 T > G polymorphisms may be associated with the development of JIA. Further and large cohort studies are needed to elucidate the precise role of these polymorphisms in the pathogenesis of JIA.