IPEX (immune dysregulation, polyendocrinopathy, enteropathy, and X-linked) syndrome is a rare immune disorder characterized by endocrinopathy such as insulin-dependent diabetes and hypothyroidism, intractable diarrhea, and recurrent infections. The mutation of the gene encoding a transcription factor, forkhead box P3 (FOXP3), leads to the dysfunction of regulatory T cells, resulting in systemic autoimmunity. IPEX syndrome is inherited in an X-linked recessive pattern. We report the case of a 12-year-old Japanese girl with IPEX syndrome. She developed severe and prolonged diarrhea with significant weight loss at age ten and was diagnosed with Crohn's disease by endoscopic and pathological finding at age twelve. Her diarrhea responded to corticosteroids, but recurred with tapering of corticosteroids. Eventually, infliximab was initiated to control her diarrhea with fair response. Having suffered from insulin-dependent diabetes since age two with hypothyroidism developing one year later, her clinical symptoms were quite reminiscent of IPEX syndrome. Although flow cytometry analysis revealed low expression of Foxp3 in CD4(+)CD25(+) T cells compared with healthy controls, no genetic mutation was found in the FOXP3 gene. In contrast to previously reported cases of IPEX syndrome without FOXP3 mutations, our patient was distinct in having had no episodes of recurrent infections.