Background The cerebellum is a brain region recognized primarily in the coordination of movement and related accessory motor functions. In addition, emerging evidence implicates the cerebellum in cognitive processes and suggests that this brain region may be subject to experience-dependent plastic changes in structure. Therefore, the aim of this study was to evaluate the role of early environmental deprivation in the maturation of the cerebellum and aspects of cognitive development. Methods Structural MRI volumes of 12 cerebellar sub-regions from 31 previously-neglected and 30 typically developing children were compared to subjects’ corresponding neuropsychological test scores. Results Neglected children had smaller volume of the superior-posterior cerebellar lobes. Moreover, superior-posterior lobe volume was found to mediate neuropsychological test performance differences between groups, with larger volumes yielding better outcomes on tests of memory and planning. Conclusions These data support the importance of experience-dependent plastic changes in cerebellar structure and highlight the role of the cerebellum in higher cognitive functions.