Steno-occlusive carotid artery disease causes increased pressure, retrograde blood flow, luminal enlargement, vascular wall thinning, elongation, convolutions, vascular re-modelization, and aneurysm formation in basilar arteries. We investigated if gender affects the severity of histomorphologic alterations of basilar arteries after bilateral common carotid artery ligation. Material and Methods: This study was conducted on 7 male and 7 female rabbits. Two of both male and female rabbits were used as a control group and the remaining were used as the study group. Permanent ligation of the common carotid arteries from just proximal of bifurcation was performed to replicate steno-occlusive carotid artery disease. Basilar artery volumes were measured by stereological methods after the sacrifice of the animals at the end of the 3rd week. Results were compared Mann-Witney U test between groups. Results: Luminal enlargement, wall thinning, elongation, convolutions, and doligoectatic configurations were detected in the majority of basilar arteries. The mean basilar arterial volume values were estimated as male rabbits were 3.65 ± 0.35 mm3 in control and 4.96 ± 0.99 mm3 in the study group. The mean basilar arterial volume values were estimated as female rabbits were 3.97 ± 0.40 mm3 in control and 6.32 ± 1.13 mm3 in the study group. The severity of basilar enlargement was significantly higher in the female rabbits compared with the male rabbits (p < 0.01). Conclusion: Bilateral common carotid artery ligation causes more severe luminal enlargement, wall thinning, elongation, convolution, and aneurysm formation in female rabbits than males.