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Background  Premature ovarian failure (POF) has repeatedly been associated to X-chromosome deletions.  FMR1  gene premutation allele's carrier women have an increased risk for POF. We intent to determine the cause of POF in a 29 year old female, evaluating both of these situations.    Methods  Concomitant analysis of  FMR1  gene CGG repeat number and karyotype revealed an X-chromosome terminal deletion. Fluorescence  in situ  further characterized the breakpoint. A methylation assay for  FMR1  gene allowed to determine its methylation status, and hence, the methylation status of the normal X-chromosome.    Results  We report a POF patient with a 46,X,del(X)(q26) karyotype and with skewed X-chromosome inactivation of the structural abnormal X-chromosome.    Conclusions  Despite the hemizygosity of  FMR1  gene, the patient does not present Fragile X syndrome features, since the normal X-chromosome is not subject to methylation. The described deletion supports the hypothesis that haploinsufficiency of X-linked genes can be on the basis of POF, and special attention should be paid to X-linked genes in region Xq28 since they escape inactivation and might have a role in this disorder. A full clinical and cytogenetic characterization of all POF cases is important to highlight a pattern and help to understand which genes are crucial for normal ovarian development.

X-chromosome terminal deletion in a female with premature ovarian failure: Haploinsufficiency of X-linked genes as a possible explanation