Background Immunodysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is a rare disorder characterised by multiple autoimmunity. Mutations in the fork head box P3 (FOXP3) gene, in chromosome Xp11.23, result in reduced numbers or a complete absence of CD4⁺regulatory T (Treg) cells and therefore in a variety of clinical presentation.

Methods We present the case of a 3-year old male with clinical and laboratory findings of IPEX and a novel mutation of the FOXP3 gene.

Results A 3-year Chinese male was admitted to the 3rd Clinic of the First Paediatrics of University of Athens, Greece, due to critical malnutrition. Severe diarrhoea and malabsorption were the predominant symptoms; therefore the administration of long term TPN was essential. The patient underwent a colonoscopy which revealed autoimmune enteropathy, while Diabetes type I, the other major clinical finding, required strict dietary program and insulin administration. Our patient was set on steroids and azathioprine, which was withdrawn however due to cholestasis on day 107.

Patient’s laboratory findings were constant with immunodeficiency (low immunoglobulins IgA and IgM), nevertheless, the flow cytometry revealed normal number of CD4⁺/CD25⁺ regulatory cells.

Under the strong suspicion of IPEX syndrome, a molecular analysis was performed and a novel mutation, c.1161G-p. H387Q in FOXP3 gene was identified, confirming the diagnosis.

Conclusions A total of 13 allelic variants in FOXP3 have been described so far, leading into different phenotypes of IPEX syndrome. The genetic variant c.1161G has been associated with hepatocellular carcinoma in Chinese population, but has never been reported in IPEX syndrome.