The mouse model for megencephaly, mceph/mceph, carries a truncating deletion in the Shaker-related voltage gated potassium channel gene 1. Affected mice display neurological disturbances and motor dysfunctions. Symptoms begin to show at 3–4 weeks of age. The cause of the brain enlargement is not clear. To elucidate early events in the development of the disease we used magnetic resonance imaging (MRI) to quantify, over time, the increase in size of several discrete brain regions in the same mice at 3, 8 and 12 weeks of age. We also analysed markers for neuropeptides and growth factors to explore their possible involvement at an early stage. The results show an enlargement of the total coronal area of the brain already at 3 weeks of age. Total brain volume, ventral cortex, hippocampal formation and cerebral cortex were enlarged at 8 weeks and onwards. Thalamus, brainstem, cerebellum and spinal cord did not differ from controls even at 12 weeks. We also report distinct disturbances in the expression of brain-derived neurotrophic factor, insulin-like growth factor binding protein 6 and several neuropeptides at 2 and 3 weeks of age, that is, before an obvious behavioural phenotype can be observed. These results provide an objective description of the size changes in different brain regions of the mceph/mceph mouse, and suggest that certain molecules could be involved in the early processes underlying these changes.