Congenital aberrations of female children's external genitalia are common worldwide with varied mode of presentation especially in regions with poor awareness. This prospective experience between July 2004 and June 2008 at two Nigerian healthcare facilities is on the mode of presentation and challenges of management of female children with ambiguous genitalia. Congenital adrenal hyperplasia (CAH) 19 (47.5%), female pseudohermaphroditism 20 (50%) and vaginal atresia 1 (2.5%) manifested as aberrations of external genitalia of 40 female children who presented between the ages of 3 months and 16 years (average 9 years). Cultural influence, lack of awareness, inadequate examination of external genitalia at birth and lack of diagnostic facilities resulted in late presentation and diagnosis with all the cases of CAH and pseudohermaphroditism raised as males. Five cases who developed female secondary sexual characteristics at puberty attempted suicide before presentation. Gender reassignment and feminizing genitoplasty were major challenges, but outcomes were encouraging.