Fragile X syndrome is one of the most common forms of inherited mental retardation and is caused by the expansion of the CGG trinucleotide repeats in the FMR-1 gene. This study was aimed to facilitate the molecular screening of fragile X syndrome in Korean children with mental retardation of unknown etiology. The subjects were tested by Expand Long Template PCR system in the presence of 7-deaza-dGTP, and then by Southern blot analysis. The PCR method provided rapid and reliable results for the identification of fragile X negative and positive patients. One hundred one mentally retarded children (78 males and 23 females) were screened by PCR amplification, which detected only one abnormal sample. The PCR-positive case was confirmed by the CGG repeat expansion on Southern blot analysis with a positive cytogenetic result. In conclusion, Expand Long Template PCR may be used as the first screening test for detecting the fragile X syndrome.