Objective: The aim of this study was to optimize the diagnosis of the fragile X syndrome in six large families with fragile X syndrome in Turkey. Methods: Southern blot analysis was performed to identify the mutations of the FMR 1 gene localized on FRAXA locus using StB12.3 probe among 36 members (19 males, 17 females) of fragile X families and controls (8 males, 8 females) following cytogenetic analysis by fragile X induction methods. Results: Eleven males and 9 females had full mutations, while 7 males and 3 females had normal range of CGG repeats. One female who was found positive by cytogenetic analysis had mosaic mutation (Y2[II-3] with 6.0, 5.2, 2.8 kb fragment sizes). Five females had premutations and 1 male had atypical fragment pattern. Conclusion: We suggest that, diagnosis of fragile X syndrome is not possible only by cytogenetic analysis. For appropriate counseling it is recommended that all members of the fragile X family under risk should be screened both by cytogenetic and molecular methods.