To improve the initial assessment of ambiguous genitalia in infants. Using a specially devised scoring system, the external genitalia (external masculinization score, EMS, range 0-12) and internal reproductive structures (internal masculinization score, IMS, range 0-10) were assessed in 426 male newborns and 291 cases of ambiguous genitalia. In normal male newborns, the median (10th centile) EMS was 11 (10). In the affected infants, the sex of rearing was male in 202 and female in 89 cases, respectively. The median (10-90th centile) EMS in those cases reared male, at 3.5 (2-8), was significantly higher than in cases reared as females, at 2 (1-6) (P < 0.001). The median IMS in cases reared as males and females was the same, at 10, but the scatter of values was higher for males (10-90th centile, 4-10) than for females (0-10) (P = 0.01). Infants reared as females were more likely to have a micropenis, a uterus and/or a urogenital sinus, but there were 12 cases where the sex of rearing was male despite the presence of a uterus; five infants without micropenis were reared as female and 23 with a urogenital sinus were reared as male. The masculinization score provides a standardized format to summarize clinical features in newborn infants with ambiguous genitalia. Gender assignment does not solely depend on the appearance of the external genitalia and the nature of internal sexual organs.