Minimal change nephrotic syndrome (MCNS) in children is frequently associated with allergy and immunoglobulin E production. T helper subtype 2 cytokines, such as interleukin (IL)-4 and IL-13, may have an important role in the development of atopy. We investigated the association of genetic variations of IL-4 receptor alpha chain (IL-4Ralpha), IL-13 and signal transducer and activator of transcription 6 (STAT6) genes with MCNS. We analyzed these polymorphisms in 85 Japanese children (55 males, 30 females) with MCNS and 127 healthy controls with neither allergic nor renal diseases. Genomic DNA was extracted from peripheral blood leukocytes. The single nucleotide polymorphisms of IL-4Ralpha (Ile50Val) and IL-13 (R130Q) were detected by primer-specific polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism analysis, respectively. GT repeat polymorphism in STAT6 gene exon 1 was investigated by fragment length analysis. A significant difference in allelic frequencies in the STAT6 gene was detected between the MCNS and control groups. There was no significant difference between the two groups for genetic variations of IL-4Ralpha and IL-13 genes. We found a significant difference in IL-4Ralpha gene polymorphism between MCNS subgroups divided according to the number of relapses. These results suggested that the genetic variation in the first exon of the STAT6 gene may be associated with a predisposition to MCNS and that the genetic variation in the IL-4Ralpha gene may be associated with its clinical course.