Autosomal recessive primary microcephaly, also known as MCPH, is a rare genetic condition where infants are born with small heads and brains. The causes of MCPH are often unknown or unclear. To date, 25 genes have been found to be associated with MCPH. Most of these genes serve similar roles in maintaining genome stability, being associated with centrosome and spindle function, chromosome dynamics, cell cycle regulation, cell division, brain development, neurogenesis, and/or the DNA damage response. In this review, we classify MCPH-associated genes based on their known functions, and propose potential novel functions of MCPH genes in DNA replication and/or the DNA replication stress response, and tumorigenesis. This classification provides a novel perspective on the underlying causes of MCPH and a comprehensive reference for future research.