Introduction: 46, XY disorder of sex development (DSD) due to 17_HSD3 gene mutations are rare. This mutation affects male external genitalia development due to inadequate production of testosterone leading to different phenotypic presentations. Most of them are born with female appearing external genitalia. Case presentation: 10-month-old baby registered as a female born to non-consanguineous healthy parents was brought with concerns regarding external genitalia from 1 month of age. Baby had a 2 cm phallus, palpable testes in the labio-scrotal folds with a perineal urethra and a vaginal orifice. Baby did not have any other health concerns and was thriving developmentally normal child. Ultrasound scan revealed undescended testes with normal echo texture without mullerian structures. Karyotype – 46,XY ,t(7;16)(q31;q24) Genetic test which confirmed compound heterozygous pathogenic variant in HSD17_3 gene. Examination under anaesthesia showed separately opening external urethral meatus and blindly ending 3cm vagina without a uterine cervix. Conclusion: Management of this patient, registered as a female led to many challenges such as gender reassignment, changing the birth certificate and complicated surgical interventions. The family was provided with psychological support .Parents made the decision of gender reassignment with courage however the changing the birth certificate remains complicated. Appropriate neonatal examination would have prevented this complication. The child is awaiting hypospadias repair. Not all parents are able to spend on genetic tests which help to understand the aetiology 46,XY DSD. There may have been many such patients undiagnosed and this is the first genetically confirmed patient from Sri Lanka.