According to the neuro-hormonal theory, sexual orientation in humans develops in the womb under the influence of sex hormones. In this article, we review the evidence from basic research on the possible role of neurotransmitters on influencing sexual orientation. We show that pharmacological or genetically induced changes in neurotransmitter systems during development might, by hormone-mediated structural and functional brain changes, result in alterations in sexual preference in animal models. We propose that in humans this mechanism may contribute to the relationship between non-heterosexual orientation and increased prevalence of neuropsychiatric disorders. Data to support this idea are reviewed. We suggest that altered neurotransmitter levels during development will increase the chance for both non-heterosexual differentiation of the brain and neuropsychiatric disorders. This possibility may have clinical implications, because medication given to a pregnant woman may, in this way, alter brain development of the fetus in a permanent way.