The regulatory IL-10 and TGF-β1 cytokine gene polymorphisms have been associated with allergic diseases in different populations, like Caucasian, Chinese and Indians. We investigated the association between the polymorphisms IL-10 A−1082G, C−819T, C−627A and TGF-β1 T+869C, G+915C, C−509T and food allergy in Japanese children. One hundred and eleven children with food allergy and 115 atopic control children without food allergy were recruited. DNA samples from these subjects were genotyped by using PCR. The odds ratio of IL-10 −1082 AA genotype was 2.5 (95% CI, 1.0–6.4) for food allergy risk when compared with atopic control subjects (p = 0.03). There were no significative differences in the frequency of TGF-β1 gene polymorphisms between both groups. Our results indicate that IL-10 A−1082G gene polymorphism is associated with food allergy susceptibility in atopic Japanese children.