It has become clear that a sexual brain dimorphism exists between males and females and animal studies have shown specific circuits developing depending on the sex. Since the first studies by Gorski, in rats, characterizing a sexually dimorphic nucleus in the pre optic area (SDN-POA) it has been accepted that the male sex imprint is done by estradiol, locally converted from testosterone through the action of a local aromatase. The presence of estradiol inhibits the apoptosis of the cells of SDN, making it bigger in the male sex. Other CNS regions have shown sexual dimorphism and we need a marker to allow us to identify these structures and, eventually, apply this information to clinical practice. In intersex patients, it may be of value to know which the brain sex of the patient is, since we have had many doubts in choosing the sex of rearing in many of these patients. It has not been uncommon that sexual inadequacies have occurred in some patients, causing a lot of discomfort and suffering for the patient himself as well as to his family. The progression of the knowledge in the field of brain sex may bring us another tool to deal with difficult cases of sex assignment in intersex patients.