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In the first several weeks after fertilization, the embyro develops rudimentary sex organs, which are crucial to the development of internal and external genitalia. In the male, if these early testes fail to develop before 8 weeks gestation, the baby will have female genitalia.
However, if the testes are lost after the critical phase of male differentiation between 12 and 14 weeks, the baby will have normal male internal and external genitalia (penis and scrotum), but the testes will be absent. This is known as congenital anorchia, or the "vanishing testes syndrome."
The specific cause is unknown, but in some cases genetic factors are apparent.