Primary amenorrhoea refers to the absence of menarche by the age of 16-18 years in the presence of secondary sexual characteristics, and occurs in 1-3% of women of reproductive age. To study the prevalence of chromosomal abnormalities and the different options available for clinical management of women in Mexico with primary amenorrhoea, a cross-sectional study was conducted in 187 women with primary amenorrhoea referred from Department of Reproductive Medicine of Morones Prieto Hospital, IMSS in Monterrey, Mexico during 1995-2003. Peripheral blood lymphocytes were cultured for chromosomal studies by the standard methods. Numerical or structural abnormalities of the sex chromosome were found in 78 women (41.71%). These women were classified into four categories: X-chromosome aneuploidies (22.99%: 12.83% pure line and 10.16% mosaicism association with a 45, X cell line); presence of chromosome Y (10.70%); structural anomalies of the X chromosome (4.28%); and marker chromosomes (3.74%). In conclusion, the prevalence of chromosomal abnormalities in Mexican women with primary amenorrhoea is within the range (24-46%) reported in world literature. Chromosomal analysis is absolutely necessary for appropriate clinical management of these patients.