We report two female patients with gonadal dysgenesis and sex chromosome mosaicism involving the Y chromosome. Conventional karyotyping was supplemented with fluorescent in situ hybridisation techniques in order to confirm the presence of Y chromosomes. One patient is a phenotypic female with karyotype 45,X/46,X,idic(Y)(q11.2). She underwent a laparoscopic gonadectomy at which streak ovaries without evidence of gonadoblastoma were removed. The second patient presented as a virilised female with karyotype 45,X/47,XYY. At laparoscopy, she was found to have mixed gonadal dysgenesis with a gonadoblastoma in situ. We recommend early gonadectomy in female children presenting with gonadal dysgenesis and the presence of a Y chromosome although once the gonadoblastoma locus on Y chromosome gene has been cloned it may be possible to identify those patients who have a low risk of developing gonadoblastoma.