The phenotypic variability observed in DSD patients depends on many factors including the presence of SRY gene, the structural rearrangement and the presence of chromosomal mosaicism, especially 45,X cell line. The phenotypic sex strongly depends on the percentage of Y chromosome and 45,X cells in the developing gonads. The aim of work was to detect sex chromosomal mosaicism in gonads and to elucidate correlation between phenotype and karyotype of patients. We reported on ten patients with variable presentations of disorders of sex development (DSD) including ambiguous genitalia, primary amenorrhea and short stature. Conventional cytogenetics studies and fluorescence in situ hybridization (FISH) on peripheral blood and gonadal tissue was performed. Non mosaic chromosomal constitution in peripheral blood of five patients was detected, and five patients exhibited mosaic cell pattern associated with different types of sex chromosomal abnormalities including 45,X, isodicentric Y chromosome, X;Y translocation. FISH analysis on paraffin embedded or fresh cultured gonadal tissue specimens was done for all patients and showed mosaicism in eight patients and a single cell line in two patients. Our study demonstrates the importance of studying sex chromosome mosaicism in the gonadal tissue of patients showing a discrepancy between their karyotype and gonadal phenotype. We concluded that using FISH on paraffin embedded or fresh cultured gonadal tissue specimens is recommended in those patients for better understanding of the phenotype karyotype correlation.