Fragile X syndrome (FXS) may be identified by many methods, such as PCR assay and Southern blot. However, each method has its limits or shortcomings. This study explored the reliability of the rapid, convenient and inexpensive hair root fragile X mental retardation protein (FMRP ) assay in the identification of FXS.FMRP in hair roots was determined by immunohistochemistry assay in 80 healthy children, in 40 children with mental retardation of unknown etiology and in 12 family members in one pedigree of FXS. FXS was confirmed by 7-deza-dGTP PCR.There was a high expression of FMRP in hair roots (> or =80%) in healthy children. Two children were confirmed with FXS by 7-deza-dGTP PCR in 40 children with mental retardation of unknown etiology. FMRP expression was 10% and zero respectively in the two children. The other 38 children had FMRP expression of more than 80%. FMRP was not expressed in the two cases of FXS from the pedigree of FXS.Inexpensive, rapid and convenient hair root FMRP assay is reliable for the diagnosis of FXS and may be widely applied for screening and diagnosing FXS in children with mental retardation.