The underlying neurobiological factors involved in sexual orientation are largely unknown. This study investigated whether neural circuits or different cognitive processes accounted for differences in brain activation in 14 heterosexual and 14 homosexual males. Brain scans were undertaken in each subject using functional magnetic resonance imaging while they viewed different sexual stimuli, i.e. heterosexual couple stimuli (HCS), gay couple stimuli (GCS), lesbian couple stimuli (LCS) and neutral stimuli (NS). Ratings of sexual attractiveness of the stimuli were assessed. Subjective sexual arousal was induced by HCS and GCS in heterosexual and homosexual men, respectively. Sexual disgust was induced by GCS and LCS in heterosexual and homosexual men, respectively. Compared with viewing NS, viewing sexual stimuli induced significantly different brain activations, most of which had the characteristics of cognitive processes. These observations suggest that different cognitive patterns may be the major cause of different subjective responses to sexual stimuli between heterosexual and homosexual men.