Juvenile idiopathic arthritis (JIA) the most common chronic arthropathy of childhood is a diverse group of chronic arthritis diseases. The protein tyrosine phosphatase N22 (PTPN22) gene exhibits regulatory activities for both T and B cells. This study aimed to study PTPN gene polymorphism in JIA. The study included 60 children with JIA and 40 age and sex matched healthy children as controls. Patients and control groups were subjected to PTPN gene polymorphism analysis. Our findings indicated a significant difference in PTPN22 polymorphism between JIA patients and the control group (P = 0.021). Different PTPN genotypes were studied in relation to patient’s age, sex and relevant laboratory data. It was concluded that PTPN22 polymorphism is different in JIA patients than healthy controls. T allele is associated only in cases with JIA and it may be considered as risk allele for certain JIA subtypes.