Turner syndrome shows the clinic triad: short stuture, primary amenorrhea, and associated somatic malformations with an incidence of 1 in 1800 live female births. The cromosomic basis for this disorder is either entire loss of one sex chromosome (45,X) or partial loss due to a structural abnormality of X and sometimes of the Y. The importance of detecting a Y cell line in these patients is the increased risk (30%) of tumour formation (gonadoblastoma) in the dysgenetic gonads. The aim of this work was to evaluate at molecular level the sex chromosome constitution in patients with Turner syndrome with abnormal karyotypes and difficult cytogenetic comprehension. There were analyzed 26 patients, 24 of whom showed two anomalous cell lines: 1 was 45,X and the other was 46,X,r(XorY?) with unidentified small rings; a girl with a mosaic 45,X/46,Xdel (Yq11) with an apparently deleted Y chromosome long arm: a patient with a mosaic 45,X/46,X,idic(Yp11) a dicentric Y with probably point of break and union in Yp11. By polymerase chain reaction (PCR) were amplified the SRY gene, the tests determination gene(Yp11.3), the AMGL gene the amelogenin gene (Yp11.2 and Xp22.1), the Y centromere, and the Y heterochromatin region (Yq12-Yqter). By this technique was established the presence of Y in 9 patients (35%). It is unknown the precise localization of a gene that causes gonadoblastoma but it is known its presence in the Y. This fact require the impiementation of a moiecular diagnosis method in order to give a better resolution of sex cromosome anomahes. Finally, using PCR metodology these results have allowed us to redefine in some cases the medical management of our patients.