Gender identity disorder (GID) is defined as a sexual disorder characterized by strong self-identification with the opposite gender, followed by unpleasant feelings due to the birth-given gender. This paper examines the current diagnostic criteria and treatment for GID. While the etiology of GID remains unknown, several hypotheses have been proposed. We describe the evolution of the hypotheses on the etiology of GID. The possible biological pathogenesis of GID is also discussed mainly from the viewpoint of brain science. Similar to animal studies, it has been reported that fetal or neonatal gonadal steroids are responsible for sexual differentiation of the human brain, which might be related to gender identity and sexual orientation. Based upon the findings of investigations into the biological basis of GID, valuable insights into GID are suggested.