This study aimed to determine the possible etiology of ambiguous genitalia in 41 newborn infants at a referral hospital in Hofuf city, Saudi Arabia. In 46,XX karyotype patients (n = 14), congenital adrenal hyperplasia and general malformation disorder were the most common causes of genital ambiguity, while in 46,XY karyotype patients (n = 18), testosterone pathway biosynthetic defect was the most common cause even in conjunction with a generalized malformation disorder. In patients with abnormal karyotype (n = 3), 1 had trisomy 18 (47,XX) and died after 3 months and 2 had different types of mosaic Turner syndrome. The karyotype was undetermined in 6 patients. Positive family history of ambiguous genitalia was noted in 4 patients.