Background: Existing brain imaging studies, investigating sexual arousal via the presentation of erotic pictures or film excerpts, have mainly used blocked designs with long stimulus presentation times. Methods: To clarify how experimental functional magnetic resonance imaging (fMRI) design affects stimulus-induced brain activity, we compared brief event-related presentation of erotic vs. neutral stimuli with blocked presentation in 10 male volunteers. Results: Brain activation differed depending on design type in only 10% of the voxels showing task related brain activity. Differences between blocked and event-related stimulus presentation were found in occipitotemporal and temporal regions (Brodmann Area (BA) 19, 37, 48), parietal areas (BA 7, 40) and areas in the frontal lobe (BA 6, 44). Conclusion: Our results suggest that event-related designs might be a potential alternative when the core interest is the detection of networks associated with immediate processing of erotic stimuli. Additionally, blocked, compared to event-related, stimulus presentation allows the emergence and detection of non-specific secondary processes, such as sustained attention, motor imagery and inhibition of sexual arousal.