Purpose Vertebral arteries (VAs) provide blood circulation to the posterior fossa in general and are the main blood supply of the posterior fossa structures of the brain. Our aim in this study is to analyze the segmental volumetric values of cerebellar structures with the voxel-based volumetric analysis system in individuals with unilateral vertebral artery hypoplasia. Methods In this retrospective study, segmental volumetric values/percentile ratios of cerebellar lobules were calculated using 3D fast spoiled gradient recall acquisition in steady-state (3D T1 FSPGR) MRI sequence images of the brain in individuals with unilateral vertebral artery hypoplasia (VAH) and in those without bilateral VAH and any symptoms of vertebrobasilar insufficiency as the control group was evaluated in volBrain. Results The VAH group consisted of 50 (19 males/31 females) and the control group had 50 (21 males/29 females) individuals. The cerebellar lobule III, IV, VIIIA and X total volumes and the cerebellar lobule I-II, III, IV, VIIIA and X gray matter volumes were lower in the hypoplastic side than the non-hypoplastic cases and also than the contralateral side of the hypoplastic cases in the VAH group. In addition, it was found that that lobules IV and V had lower cortical thickness and lobules I-II had a higher coverage rate in the intracranial cavity in the hypoplastic side than the non-hypoplastic cases and also than the contralateral side of the hypoplastic cases (p < 0.05). Conclusion In this study, it was found that cerebellar lobule III, IV, VIIIA, X total volumes and cerebellar lobule I-II, III, IV, VIIIA, X gray matter volumes in addition to lobule IV, V cortical thicknesses were low in individuals with unilateral VAH. Being aware of these variations and taking them into account during future volumetric studies on the cerebellum are very important.