Disorders of sex development involving ambiguous genitalia present complex challenges because sex assignment decisions intersect with medical uncertainty, child rights, positive law, Islamic jurisprudence, and socio-cultural expectations. In Indonesia, the absence of DSD-specific regulations may create uncertainty regarding sex assignment, informed consent, multidisciplinary decision-making, and irreversible genital surgery. This study aims to examine the Indonesian legal framework governing sex assignment and legal protection for pediatric patients with DSD, assess its consistency with international medical standards, identify disharmony among legal, Islamic, and cultural perspectives, and formulate a harmonization framework. The study uses a normative juridical approach through library research, employing statutory, conceptual, comparative, and gap analysis methods. The findings reveal four principal regulatory gaps: the absence of DSD-specific technical guidelines, mandatory multidisciplinary team requirements, legal safeguards for deferring irreversible surgery, and mechanisms for progressive child participation. The study also identifies terminological, substantive, and operational disharmony between positive law, Islamic jurisprudence, medical standards, and socio-cultural practices. It concludes that Indonesia needs an integrated, child-centered DSD regulatory framework that emphasizes multidisciplinary assessment, DSD-specific informed consent, protection against premature irreversible interventions, and culturally and religiously sensitive family counseling to safeguard children’s long-term rights and best interests.