The G of the CHARGE association represents genital hypoplasia, which is typically recognized only in males (micropenis/ cryptorchidism). The cause of genital hypoplasia in this disorder has not been determined. We now report the cases of nine individuals with CHARGE association and hypogonadotropic hypogonadism, manifested by hypogenitalism and gonadotropins at or below minimal detectable levels at ages when these hormones should be readily measurable. We suggest that central hypogonadism is responsible not only for the genital hypoplasia in male patients but also for the lack of secondary sexual development in patients of both sexes. Since hypogonadotropic hypogonadism appears to be the usual cause of genital and pubertal abnormalities in CHARGE association, measurement of serum luteinizing hormone (LH) and follicle-stimulating hormone (FSH) concentrations in infants up to 2-3 months of age who are suspected of having this disorder could help establish the diagnosis. Determination of serum LH and FSH concentrations in teenagers with CHARGE association could result in early diagnosis of hypogonadotropic hypogonadism, allowing for treatment of hormonal deficiencies and minimization of potential secondary psychosocial and medical problems.