Objective To explore the characteristics of WAS gene mutation in Wiskott-Aldrich syndrome (WAS). Methods The clinical data of one infant with WAS were retrospectively analyzed. All exons and flanking sequences in WAS gene were detected by PCR. Results A 5-month-old boy, who has a history of eczema and recurrent infection, was hospitalized for thrombocytopenia. CD8+ and CD4+ T cell were increased while CD19+ B cell was normal. Bone marrow cytology suggested megakaryocyte mature hindrance. WAS gene detection found C.880 A?>?G (p.Ile294Val) mutation, but no mutations were found in parents. This site was a pathogenic mutation predicted by Polyphen 2 software and SIFT software. Besides, sequence conservation analysis of different species found it was a conservative site and structural prediction analysis revealed it may affect the normal protein structure. This site of mutation has not been reported before. Conclusions Gene detection can make early diagnosis of WAS and C.880 A?>?G (p.Ile294Val) is a new mutation.