To evaluate the implication of chromosome abnormalities in the etiology of premature ovarian failure (POF), 1000 patients with POF recruited at the Department of Cytogenetics of Farhat Hached Hospital (Sousse, Tunisia) between January 1996 and December 2008. Chromosome analyses were performed by using karyotyping and interphase fluorescent in situ hybridisation (FISH) using a centromeric probe of the chromosome X to look for low-level mosaicism of X-chromosome monosomy. Hundred and eight chromosomal abnormalities (10.8%) were found using karyotype analysis. Anomalies were detected in 61 cases out of 432 primary amenorrhea patients (14.12%) and 47 cases out of 568 secondary amenorrhea patients (8.27%). In 23 POF patients among 200 (11.5%) with 46,XX normal karyotype and explored using interphase FISH analysis, the percentage of cells with X-chromosome monosomy was significantly higher as compared with controls in the same age. The cytogenetic study of POF patients showed a high prevalence of chromosome anomalies either in primary or in secondary amenorrhoea. Mosaic X-chromosome s aneuploïdy was the most frequent abnormality and some patients with POF may be attributable to low-level 45,X/46,XX mosaicism detectable using FISH analysis.