Fragile X syndrome results from the unstable expansion of a CGG repeat within the FMR1 gene. Three classes of FMR1 alleles have been identified, normal alleles with 6-60 repeats, premutations with 60-200 repeats, and full mutations with > 230 repeats. Premutations are exquisitely unstable upon transmission. Normal alleles, while generally stable upon transmission, are thought to have different intrinsic mutation frequencies, such that some normal alleles may be predisposed towards expansion while others may be more resistant to such change. One variable that may account for this difference is the occurrence of one or more AGG triplets punctuating the normal CGG repeat. The AGG interruptions lead to alleles that have equivalent overall length but different lengths of perfect repeats. To test the influence of the length of perfect repeats on stability, we examined the CGG repeat of single sorted sperm from two males, each with 39 total repeats, but distinct AGG interruption patterns. Sorted sperm of each donor showed -15% variation in repeat length, consistent with previous studies of sorted sperm at other triplet repeat loci. However, when discounting the majority variation of +/-1 repeat, the male with 29 perfect repeats showed 3% expansion changes while the donor with only 19 perfect repeats had none (< 0.9%). Moreover, > 90% of all variant sperm, including all those observed with expansions, showed expansion or contraction of the 3' end of the repeat array. These data are consistent with the hypothesis that perfect repeat tracts influence the repeat stability and that changes of the FMR1 repeat exhibit polarity.