Mixed gonadal dysgenesis with 45,X/46,X,idic(Y)/46,XY,idic(Y) karyotype: To present the new karyotype with mixed gonadal dysgenesis, the aetiologic approach and difficulties in genetic counseling in mosaic sex chromosome disorders. We report a fourteen-year-old boy presented with slightly ambigious genitalia. Cytogenetic and fluorescence in situ hybridization investigations were carried out on his peripheral lymphocytes. As a result, three cell lines, 45,X, 46,X,idic(Y)(q11.2) and 46, XY were observed. A markedly higher percentage of Y-containing cells was observed in the blood (68%), which was not considered to be the major reason why the case did not have distinct ambiguous genitalia. We suggest that study of cytogenetic and molecular mosaicism involving sex chromosomes may help to further unravel the mysterious process in mixed gonadal dysgeneic patients.