Background: In this epidemiological study, we sought to capture the incidence of ambiguous genitalia in neonates and to describe initial management strategies. Methods: We used the registry for rare diseases in pediatrics in Germany to ascertain cases and asked reporting institutions for information on phenotype, laboratory tests, imaging results, diagnosis, initial management and sex assignment. Results: We identified 80 cases within a 2-year study period and calculated an incidence of 2 per 10,000 births with ambiguous genitalia per year in Germany. Prevalence was higher in infants from non-German family background. In more than 50% of all infants a definite diagnosis was lacking even at the age of 6 months. In those cases where the etiology was confirmed, the most common diagnosis was congenital adrenal hyperplasia, followed by androgen insensitivity syndrome and mixed gonadal dysgenesis. Associated malformations were very common, affecting 37.5% of all infants. Sex assignment was female in 46,XY infants with predominately female phenotype and all 46,XX infants. Early surgery was performed in many cases irrespective whether a definite diagnosis had been established or not. Integrated psychosocial care was the exception rather than the rule. Conclusions: Classification and management of ambiguous genitalia at birth remain a challenge for all professionals involved. National and international registries may help to provide a better understanding of the incidence and clinical course of such disorders.

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