Background: Prophylactic gonadectomy can only be proposed to patients at risk of gonadal germ cell tumors (GGCTs) in disorders of sex development (DSDs) patients. However, this does not justify prophylactic gonadectomy given that they are uncommon and nearly always benign. In these cases, the survival rate of a malignant GGCT is better (approximately 95% at 5 years), but, chemotherapy also has its own lifelong side effects such as metabolic syndrome and cardiovascular risk. Case presentation: This paper highlights 2 cases of young individuals aged 16–22 years who presented to KJK Hospital, Thiruvananthapuram with amenorrhea. After initial clinical and routine hormonal and radiological investigation, they were diagnosed with Androgen insensitivity syndrome and Mosaic Turner syndrome respectively on karyotyping. After discussing the condition and options of treatment with the patients and family, laparoscopic prophylactic gonadectomy was planned and performed, with removal of bilateral undescended testes and streak ovary in respective cases followed by hormonal replacement therapy. Conclusion: Usually, the external genitalia in DSD are normal which makes it difficult to diagnose before puberty without any significant clinical indication. In our cases, it demonstrates that mere physical or clinical examination will not be sufficient to identify such cases. Therefore, in females with amenorrhea, genetic testing should be performed along with a general examination. The procedure risks are very low, as laparoscopic gonadectomy can be done as a daycare procedure and can be performed in 30–60 minutes duration with no visible scar. Added benefits of Laparoscopy include a provision to take biopsies or do gonadopexy. It is always advised to postpone gonadectomy till puberty as it allows spontaneous puberty, and allows informed decision-making by the patient.