Background: Cancer, trauma, infection, or radiation can cause perineal defects. Fasciocutaneous flaps based on perforator vessels (PV) from the internal pudendal artery (IPA) provide an ideal reconstructive option for moderate defects. We hypothesized that, due to gender differences in the pelvic-perineal region, the anatomical distribution of PV differs between genders. Methods: Computed tomography angiographies from male and female patients without pelvic-perineal pathologies were retrospectively analyzed to study the vascular anatomy of the IPA. The number, size, type, and distribution of PV were recorded and compared between genders. Four anatomical regions were defined to describe the distribution of PV on each perineal side: anterior (A), anterior-central (AC), central-posterior (CP), and posterior (P). Results: A total of 63 computed tomography angiographies were analyzed (men, 31; women, 32). Each IPA provides 2 +/- 1 PV and 5 +/- 2 terminal (cutaneous) branches: in both genders, 85% of PV are septocutaneous (15% musculocutaneous). In women, 70.5% of PV are located in AC, 28.2% in CP, 1.2% in A, and 0% in P: average diameter of the PV is 2.4 +/- 0.3 mm. In men, 53.7% of PV are located in CP, 43.1% in AC, 3.3% in A, and 0% in P: average diameter of the PV is 2.8 +/- 0.5 mm. Gender-specific differences in anatomical distribution of PV are significant (P < 0.001). Conclusions: Number, size, and type of terminal branches of PV of the IPA are consistent between genders, but their distribution is different, with women having an anterior predominance. Knowledge of gender-specific anatomy can guide preoperative planning and intraoperative dissection in flap-based perineal reconstruction.