In the last decade functional imaging has gained substantial importance for identifying cortical and subcortical brain regions being involved in the micturition circuit. However, possible gender differences are still a matter of debate. In the present study we used functional magnetic resonance imaging (fMRI) to determine micturition related brain regions in healthy men and compared them with those in women to elucidate gender-related differences. fMRI was performed at 3 T in 12 healthy men with urge to void due to a filled bladder. In a non-voiding model they were instructed to contract or to relax the pelvic floor muscles repetitively. As previously reported in women, contraction and relaxation of pelvic floor muscles induced strong activations in the brainstem and more rostral areas in our group of healthy men. In general, men had stronger activations during contraction than women in nearly all identified areas. In contrast, results for the relaxation condition were similar. Some of the differences between contraction and relaxation, formerly detected in females, could be found in our group of males as well. The results suggest that in women and men the same cortical and subcortical networks exist for micturition control. Especially, the well located activations in the putative pontine micturition centre and the periaqueductal grey could be identified in both sexes. However, pelvic floor muscle control seems to induce different activation intensities in men and women.