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Fragile X syndrome is the most common form of inherited mental retardation. The molecular basis is usually the unstable expansion of a CGG repeat in the FMR1 gene. We previously analyzed a sample of two Basque valleys. In the present work we extend the study to another five isolated valleys. The results show that differences in factors implicated in CGG repeat instability—CGG repeat size, XS548/FRAXAC1 haplotypes, and AGG interspersion pattern—are present in the Basque populations analyzed.