Autosomal recessive primary microcephaly (MCPH) consists of a group of disorders characterized by microcephaly and intellectual disability. This study is essential to complement previous findings of MCPH as it helps clarify the role of different genes and proteins involved in the underlying pathophysiology of MCPH. To date, 27 different mutations have been identified. This study defines a number of changes in gene expression occurring in MCPH. This helps deepen our understanding of the effect of MCPH mutations on gene expression. This study also shows the functions of proteins that increase, are unaffected or become dysfunctional due to MCPH. We identified a marked reduction of about 30 proteins with vital roles in several processes including cell cytoskeleton dynamics, cell cycle progression, ciliary functions, and apoptosis. We used Cdk5rap2 (Hartwig’s anemia mice (an/an)), which is a model that closely represents MCPH3. Gel electrophoresis was utilized in order to separate brain proteins. Fixation and protein identification was then done in order to detect changes in the level of the tested proteins