Factors related to sexual arousal are different in men and women. The conditions for women to become aroused are more complex. However, the conventional audio-visual stimulation (AVS) materials used to evaluate sexual arousal are universal. In the present study, we investigated sexual differences in the response to different types of AVS by studying activated areas of the brain using functional magnetic resonance imaging (fMRI). fMRI was performed during two types of AVS in 20 healthy heterosexual volunteers (aged 20–28 years, 10 men and 10 women). The two AVS types were:(1) mood type, erotic video clips with a concrete story and (2) physical type, directly exposing sexual intercourse and genitalia. fMRI images were analyzed and compared for each stimulation with a Mann–Whitney U test, with statistical significance set at P< 0.05. Men preferred the physical type of AVS to the mood type (mean arousal score 2.14 vs 1.86 in females) and women preferred the mood type (mean arousal score 2.14 vs 1.86 in males)(P< 0.05). Degrees of activation in brain areas differed between genders and types of AVS for each gender. This should be considered when applying the AVS method to evaluate and diagnose female sexual dysfunction.