The fragile X mental retardation syndrome is caused by the expansion of an unstable CGG repeat in a 5' exon of the FMR1 gene. Significant linkage disequilibrium between this mutation and flanking microsatellite markers has been observed previously in Caucasian populations, a very unusual finding for an X-linked disease which severely impairs reproduction fitness in affected males. This reflects the multistep process at the origin of the full mutation. We have analyzed the FRAXAC2 and DXS548 microsatellites in 26 fragile X families originating from various parts of Finland, and report a striking founder effect much stronger than the linkage disequilibrium observed previously in other more heterogeneous populations. One DXS548 allele was present on 92% of fragile X chromosomes and on 17% of normal chromosomes. A single haplotype accounted for 73% of fragile X chromosomes,and was found only once in 34 normal chromosomes, corresponding to a relative risk of about 90 compared to its absence. The broad geographic origin of the high-risk haplotype and its expected frequency suggest that it was present in initial settlers of Finland, and could thus have been carried silently through 100 generations.