To determine if FRAXE alleles may have haplotype associations with nearby microsatellites, we analyzed 149 unrelated control Caucasian X chromosomes for FRAXE GCC alleles along with five nearby microsatellites. The microsatellites included three that are new; GT25, CA4, and CA5 located approximately 24, approximately 48, and approximately 50 kb proximal to the FRAXE GCC repeat, and two that were identified previously: DXS8091 and DXS1691, located approximately 90 and approximately 5 kb distal. No significant correlations between haplotypes for the proximal microsatellites were found. Significant correlations of FRAXE GCC repeats and distal microsatellite allele sizes, DXS8091 (r = 0.24) and DXS1691 (r = -0.40), were found. One haplotype, 18-19 of DXS8091-DXS1691, was present on 57% of chromosomes with > or =22 FRAXE repeats but present on only 10% with <22 repeats. We conclude that this distal haplotype association likely reflects a FRAXE allele founder effect. The lack of association or founder effects seen for the three newly identified proximal markers, located within 50 kb of FRAXE GCC, may reflect an unusually high rate of mutation for these microsatellites or a higher rate of recombination in the proximal region.