The strongest sex differences on any cognitive task, favoring men, are found for tasks that require the mental rotation of three-dimensional objects. A number of studies have explored functional brain activation during mental rotation tasks, and sex differences have been noted in some. However, in these studies there was a substantial confounding factor because male and female subjects differed in overall performance levels. In contrast, our functional brain activation study examined cortical activation patterns for males and females who did not differ in overall level of performance on three mental rotation tasks. This allowed us to eliminate any confounding influences of overall performance levels. Women exhibited significant bilateral activations in the intraparietal sulcus (IPS) and the superior and inferior parietal lobule, as well as in the inferior temporal gyrus (ITG) and the premotor areas. Men showed significant activation in the right parieto-occitpital sulcus (POS), the left intraparietal sulcus and the left superior parietal lobule (SPL). Both men and women showed activation of the premotor areas but men also showed an additional significant activation of the left motor cortex. No significant activation was found in the inferior temporal gyrus. Our results suggest that there are genuine between-sex differences in cerebral activation patterns during mental rotation activities even when performances are similar. Such differences suggest that the sexes use different strategies in solving mental rotation tasks.