As abundant types of genetic predisposition and environmental factors seem to be associated with the development of juvenile-onset systemic lupus erythematosus (JSLE), we investigated the gene polymorphisms of two anti-inflammatory cytokines, including interleukin-10 (IL-10) and transforming growth factor-beta (TGF-β), which were previously found to be associated with SLE in adults, in a group of patients with JSLE. We studied a group of 59 Iranian patients with JSLE in comparison with 140 healthy controls and assessed the frequency of alleles, genotypes, and haplotypes of IL-10 and TGF-β single-nucleotide polymorphisms (SNPs) using polymerase chain reaction with sequence-specific primers method. The CA genotype was significantly more frequent at position -592 in IL-10 in patients with juvenile-onset systemic lupus erythematosus than in the controls (P = 0.01). Genotype CC was detected at the same position in 32.7 % of the patients; this frequency was significantly lower than the frequency of 50.7 % recorded in the healthy controls (P = 0.03). The TC haplotype of TGF-β (codon 10, codon 25) was significantly more frequent in the patients with juvenile-onset systemic lupus erythematosus than in the healthy controls (P = 0.02). Nevertheless, these significant associations disappear after Bonferroni correction. Our findings suggest that IL-10 (-1082, -819, -592) and TGF-β (codon 10, codon 25) gene variants may not be associated with the development of JSLE in Iranian population.