Objective: The presence of Y chromosome in patients with gonadal dysgenesis is related to the risk of gonadoblastoma. Since the patients with abnormal sexual differentiation may have cryptic Y mosaicism, it is important to detect the presence of Y material in these patients. But sometimes it is difficult to detect Y material only with karyotyping. This study was performed to evaluate the usefulness of the SRY gene screening in blood and gonad by using PCR in detecting the presence of Y material and possible tissue mosaicism in patients with gonadal dysgenesis as Turner syndrome and 46,XY pure gonadal dysgenesis (PGD, Swyer syndrome). Method: In 26 patients with gonadal dysgenesis, we screened for Y material by using PCR for SRY gene in peripheral leukocytes and in gonadal tissues of some patients. They were 22 cases of Turner syndrome (7 45,XO, 2 46,Xi(Xq), 3 45,XO/46,XX, 5 45,XO/46,Xi(Xq), 1 45, XO/46,XY, 1 45,XO/46,Xi(Yq), 1 45,XO/47,XYY, 1 46,XX,del(X)(q24) and 1 46,X,+mar) and 4 cases of 46,XY pure gonadal dysgenesis. PCR for SRY gene in the gonadal tissue was performed in 5 Turner syndrome and 2 PGD to determine the cryptic Y mosaicism between blood and gonad. Results: By using PCR analysis for SRY, Y chromosome material was detected in the blood of 4 of 22 Turner syndrome patients (45,XO/46,Xi(Xq), 45,XO/46,Xi(Yq), 45,XO/46,XY, and 45, XO/47,XYY), 3 of 4 46,XY pure gonadal dysgenesis. Discrepancy between karyotyping and blood PCR for SRY was noted in 1 Turner syndrome (45,XO/46,Xi(Xq)) and 1 PGD. Laparoscopic gonadectomy was performed in Y containing or SRY positive cases. In addition, PCR analysis for SRY in the gonads of 5 Turner syndrome and 2 PGD showed discrepancy between blood and gonad or between both gonads in 3 Turner syndrome (45,XO/46,Xi(Xq), 45,XO/46,Xi(Y q), 45,XO/46,XY) and 2 PGD patients. Conclusion: In gonadal dysgenesis, PCR analysis for SRY gene is useful to detect the cryptic Y mosaicism that is sometimes undetected by karyotyping. And since there may be tissue mosaicism, it is necessary to evaluate Y mosaicism in various tissues even in the case without Y chromosome on karyotyping.