X-linked congenital adrenal hypoplasia is characterised by the acute onset of primary adrenal insufficiency in infancy or early childhood and hypogonadotropic hypogonadism (HH) at puberty, arising from mutations of the nuclear receptor subfamily 0 group B member 1 (NR0B1) gene. This study investigated an extended family with two affected males (patient A: 23 years and patient B: 2 months old) and three carrier females. Sequencing analysis of the NR0B1 gene coding region from the family revealed a novel hemizygous deletion [c.604delT; p.(C202Afs*62)] in the two male patients. Furthermore, the patients' respective mothers and their common grandmother had this heterozygous mutation, but it was not present in the Human Gene Mutation Database. The two male patients showed inconsistent clinical features at onset, particularly in early childhood; however, it is possible that the younger patient will eventually show a delay of puberty, feminisation, and nonspermatogenesis in adulthood, similar to that in the older patient. Identification of a novel NR0B1 mutation in this family is important for the diagnosis and genetic counselling of children with primary adrenal insufficiency and HH, and will be helpful for predicting long-term clinical symptoms.