Rett syndrome (RTT) is a rare congenital disorder which in most cases (95%) is caused by methyl‐CpG binding protein 2 (MECP2) mutations. RTT is characterized by regression in global development, epilepsy, autistic features, acquired microcephaly, habitual hand clapping, loss of purposeful hand skills, and autonomic dysfunctions. Although the literature has demonstrated decreased volumes of the cerebrum, cerebellum, and the caudate nucleus in RTT patients, surface‐based brain morphology including cortical thickness and cortical gyrification analyses are lacking in RTT. We present quantitative surface‐ and voxel‐based morphological measurements in young children with RTT and Rett‐like syndrome (RTT‐l) with MECP2 mutations. The 8 structural T1‐weighted MR images were obtained from 7 female patients with MECP2 mutations (3 classic RTT, 2 variant RTT, and 2 RTT‐l) (mean age 5.2 [standard deviation 3.3] years old). Our analyses demonstrated decreased total volumes of the cerebellum in RTT/RTT‐l compared to gender‐ and age‐matched controls (t (22)=‐2.93, p = .008, Cohen's d = 1.27). In contrast, global cerebral cortical surface areas, global/regional cortical thicknesses, the degree of global gyrification, and global/regional gray and white matter volumes were not statistically significantly different between the two groups. Our findings, as well as literature findings, suggest that early brain abnormalities associated with RTT/RTT‐l (with MECP2 mutations) can be detected as regionally decreased cerebellar volumes. Decreased cerebellar volume may be helpful for understanding the etiology of RTT/RTT‐l.