In order to investigate the origin of the fragile X mutation in the Brazilian population, we assessed the size of the microsatellite markers DXS548, FRAXAC1 and FRAXAC2 in 72 X chromosomes from unrelated affected males and 64 control chromosomes. We found a significantly different distribution of alleles between fragile X and controls for loci DXS548 and FRAXAC1, but no apparent linkage disequilibrium was detected for the sequence FRAXAC2. The most frequent DXS548/FRAXAC1 haplotypes in affected males were haplotypes 204/158 bp (2-1) and 196/152 bp (6-4). These findings are in accordance with the proposed two main mutational pathways for the generation of FMR-1 alleles that predispose to instability and hyperexpansion.