We report the results of a molecular investigation of 25 patients who had Turner syndrome and who had previously been subject to analysis using cytogenetic techniques. When in situ hybridization and polymerase chain reaction (PCR) techniques were applied, a larger number of mosaic individuals were observed than were detected by cytogenetic methods. This was mainly because of the presence of the cell line 46,XX. The most frequent mosaics were 45,X/46,XX (36%); the presence of isochromosomes comprised 24% and fragments 12%. The patients who had been previously diagnosed with mosaicism displayed a higher complexity in their karyotypes because of the presence of new cellular lines. The isodicentric X chromosome for the long arm, idic(Xq), gave rise to complex mosaics of up to nine cell lines. The application of fluorescence in situ hybridization and PCR led to a clearer definition of alterations at the centromeric level and the identification of the nature of chromosome fragments.