Background: A number of studies have consistently reported that the abuse and dependence of methamphetamine can cause severe structural and functional abnormalities in the cerebral regions. It appears that fewer structural studies have examined the effect of methamphetamine on the cerebellum, whereas the interest on how addiction disorders affect the cerebellum is increasing coinciding with various studies on the important role of the cerebellum. Therefore, we initiated an experiment where we aimed to investigate the structural changes of the cerebellar gray matter in methamphetamine-dependent patients and gender differences in the effects of methamphetamine. Further, we aimed to study the relation between the cerebellar structural abnormalities and the emotional and cognitive problems in methamphetamine-dependent patients.Methods: We acquired high-resolution brain magnetic resonance imaging scans from 31 methamphetamine-dependent patients and 31 healthy comparison subjects. The density of the cerebellar gray matter was measured by a voxel-based morphometry (VBM) utilizing SUIT (Spatially Unbiased Infratentorial Template) toolbox and the structural differences between the groups were analyzed.Results: Compared to the healthy comparison subjects, methamphetamine-dependent patients showed significant reductions of gray matter density in the VIIB, VIIIA, VIIIB, CrusII regions of the bilateral cerebellar posterior lobe (left: z score = 5.03, FDR-corrected p = 0.003, right: z score = 4.84, FDR-corrected p = 0.005). Considering the gender difference, male methamphetamine-dependent patients had significantly more reductions in the gray matter density of the left cerebellar posterior lobe than female methamphetamine-dependent patients (F = 60.72, p < 0.001, p for interaction = 0.007).Conclusion: The results indicate that methamphetamine-dependent patients had structural deficits in the cerebellar posterior lobe associated with cognitive functions as well as motor and emotion control. In addition, the present study shows that males are more vulnerable than females in the effects of methamphetamine on the cerebellum and the gender difference may affect density changes in cerebellar gray matter in methamphetamine-dependent patients. Thus, these findings suggest that the cerebellar structural abnormalities are linked to methamphetamine dependence and may also support the potential correlation between the cerebellum and the disorders of methamphetamine-dependent patients.