Recent reports suggest that women with FRAXA premutations have an increased likelihood of having premature ovarian failure (POF). We screened 147 women with idiopathic POF for the number of trinucleotide repeats at the FRAXA and FRAXE loci. We found six women with FRAXA premutations, including four familial and two sporadic cases, but no women with FRAXA full mutations. At the FRAXE locus there were no pre- or full mutations but there was an excess of small alleles with fewer than 11 repeats, including at least one small deletion at or near the triplet. The association of FRAXA premutations with POF confirms that premutation alleles can affect ovarian development or function or both.