We investigated the association between IL-1beta, IL-1ra, and TNF-alpha gene polymorphisms and childhood nephrotic syndrome (NS). We analyzed the genetic polymorphism of IL-1beta, IL-1ra, and TNF-alpha genes in 152 patients with childhood NS and 292 healthy adult controls. The C to T exchange at position -511 of IL-1beta and the G to A at -308 of the TNF-alpha gene were genotyped. Five alleles of the IL-1ra gene were identified and designated as IL1RN*1, IL1RN*2, IL1RN*3, IL1RN*4, and IL1RN*5, according to the variable number of tandem repeats in intron 2. The allele frequencies of IL-1beta1 (-511C), IL-1beta2 (-511T), TNF1 (-308G), and TNF2 (-308A) were 53.0, 47.0, 92.1, and 7.9%, respectively, in the childhood NS group. This was not significantly different from normal controls. In the childhood NS group, the allele frequencies of IL1RN*1, IL1RN*2, IL1RN*3, IL1RN*4, and IL1RN*5 were 90.8, 7.6, 1.6, 0, and 0% [IL1RN*1 odds ratio (OR)=0.296, P=0.0001, IL1RN*2 OR=3.902, P=0.0002]. A high allele frequency of IL1RN*2 and a lower allele frequency of IL1RN*1 were found in childhood NS, although there was no association with IL-1beta and TNF-alpha. A high allele frequency of the IL1RN*2 allele may affect disease susceptibility in childhood NS.