Background Studies showed gender-associated differences in multiple sclerosis (MS) disease evolution and in the evolution of conventional magnetic resonance imaging (MRI) findings. Objective The aim of this study was to investigate gender differences according to a number of conventional and nonconventional MRI measures in patients with MS. Methods We examined 763 consecutive patients with MS [499 (19.2% men) relapsing-remitting (RR), 230 (24.8% men) secondary-progressive, and 34 (44.1% men) primary-progressive], 32 (21.9% men) patients with clinically isolated syndrome (CIS), and 101 (30.7% men) normal controls (NC). Patients were assessed using conventional and nonconventional MRI measures. Gender-related MRI differences were investigated using general linear model analysis, corrected for MS disease type. Results In the total MS group, male patients showed lower normalized peripheral gray matter (GM) ( P < 0.001) and normalized GM ( P = 0.011) volumes than female patients. Female patients presented lower normalized white matter (WM) volumes ( P = 0.011). These gender effects were not observed in NC. Male patients also showed more advanced central atrophy ( P = 0.022). In RRMS male patients, there was also a higher lateral ventricle volume ( P = 0.001). The GM-WM normalized ratio was lower for male patients with MS compared with male NC (0.97 vs. 1.09, P < 0.001) but not in patients with CIS compared with NC. Conclusions There were no significant gender-related differences regarding nonconventional MRI measures. GM and central atrophy are more advanced in male patients, whereas WM atrophy is more advanced in female patients. These gender-related MRI differences may be explained by the effect of sex hormones on brain damage and repair mechanisms.