Background: Autoimmune hepatitis (AIH) is an inflammatory liver disease, presenting usually with chronic hepatitis, while acute or fulminant hepatitis are not uncommon. In this study, we investigated the pro-inflammatory cytokines gene polymorphisms in a group of pediatric patients with AIH and compared the results with a group of healthy individuals.Methods: The study group was conducted in 57 pediatric patients with AIH who was referred to the Children’s Medical Center Hospital, the Pediatrics Center of Excellence in Tehran, Iran. The studied alleles and genotypes include TNF-a (A/G -308, A/G -238), IL-1a (C/T -889), IL-1b (C/T -511), IL-1 b (C/T +3962), IL-1 receptor (IL-1R; C/T Pst-I 1970), IL-1RA (C/T Mspa-I 11100), and IL-6 (C/G -174 and A/G nt565).Findings: The frequencies of the following alleles were significantly higher in AIH patients, compared to healthy controls: TNF-a A allele at position -308 (23.7% in AIH patients vs. 14.2% in controls, p<0.035), IL-6 A allele at position nt565 (35.1% in AIH patients vs. 18% in controls, p<0.00042). The most significant differences in genotype frequency between AIH patients and healthy controls belong to TNF-a AA, GA and GG genotypes at position -238 (17.5% in AIH patients vs. 0.7% in controls, p<0.0001 for AA genotype, 3.5% in AIH patients vs. 41.6% in controls, p<0.0001 for GA genotype, and 79% in AIH patients vs. 57.7% in controls, p<0.0081 for GG genotype).Conclusion: IL-6 and TNF-a polymorphisms are shown to have significant differences between AIH patients and healthy controls, but IL-1 family has no significant correlation.