Regulation of cell proliferation is of fundamental importance for growth and prevention of cancer. An obligatory step in the regulation of cell proliferation is the control of the initiation of DNA synthesis. The minichromosome maintenance (MCM) proteins are essential DNA replication factors crucial for initiating DNA synthesis once every cell cycle. Recent studies show that the level of MCM proteins is stringently regulated to correlate with cell proliferation and carcinogenesis. Here we discuss recent data, which highlights the usefulness of minichromosome maintenance (MCM) gene expression for detecting proliferating cells as well as zones containing proliferative/stem cells during embryogenesis in a whole organism.