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The aim of the present prospective study was to determine the incidence of hypospadias in newborns in one of the busiest teaching hospitals of Istanbul, and to investigate the risk factors.All live-born boys delivered between September 2007 and December 2008 were screened for hypospadias. A questionnaire was given to the parents of the hypospadias and control subjects for investigation.Out of 1750 boys examined, 34 had hypospadias, that is, the frequency was 19.4 per 1000 male live-births and 93.7 per 10 000 total live-born deliveries. The incidence of additional coexistent anomalies was 29.4%, predominantly urogenital (17.6%), the majority of which were cryptorchidism (14.7%). Twelve (35.3%) of the 34 hypospadiac boys had a second family member with a genital anomaly, nine (26.5%) of whom had hypospadias, three (8.8%) being the fathers. Mean birthweight, length and head circumference were significantly lower in the hypospadiac infants than the control group (P= 0.003, P= 0.025, P= 0.002). Although parity, parental consanguinity, hypospadias in family members, and low birthweight also varied significantly among the groups, logistic regression analysis indicated that maternal age, prematurity, coexistence of cryptorchidism and presence of genital anomaly among family members were independent risk factors for hypospadias (P= 0.016, P= 0.0001, P= 0.041, P= 0.0001, respectively).Genetic predisposition and placental insufficiency in early gestation might play a role in the etiology of hypospadias.