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<it>Objectives</it>. To study G→A −238 and G→A −308 polymorphisms in the promoter region of the tumour necrosis factor (TNF) α gene in patients with juvenile idiopathic arthritis (JIA). We analysed whether there were any associations between these polymorphisms and the type of JIA and/or the clinical course of the disease in two populations. <it>Methods</it>. The first group consisted of 51 Turkish JIA patients and the second consisted of 159 JIA patients from the Czech Republic. Healthy individuals (93 and 100) from each country served as controls. Subgroups of JIA were defined according to the Durban criteria. The course of the disease was defined on the basis of the physician's global evaluation of disease activity, the swollen and tender joint count and the erythrocyte sedimentation rate. <it>Results</it>. In both JIA cohorts, the distribution of genotypes was not significantly different among the types of JIA. The G→A −238 polymorphism did not have an effect on the patients' outcome in either group. The G→A −308 polymorphism was significantly associated with a poor outcome in the Turkish group (<it>P</it>=0.005) but there was no association in the Czech patients. Some features of JIA in Turkish patients differed from those in Czech patients. <it>Conclusions</it>. Genetic differences may accompany the phenotypic differences found in the Turkish group. Although larger numbers of patients are clearly needed to verify this, we suggest that the G→A −308 polymorphism may be operative in defining disease outcome in selected groups.