Flow cytometers are well-established tools with fundamental importance in biology and medicine to examine and identify cell populations, density, size distributions, compositions, and disease diagnosis and monitoring. Still, these devices are expensive with a low level of integration for sample preparation. Miniaturized microfluidic cytometers, i.e., microcytometers, for monitoring cells in a wide range of biological samples are currently being developed, providing more affordable and integrated solutions. Several detection methods have been developed and applied in microcytometers such as electrical, optical, and magnetic sensing techniques, which are integrated with microfluidic technology. Magnetic microcytometers present several advantages when compared to optical systems such as the fact that these devices provide more stable labeling by using magnetic nanoparticles (MNPs) or beads (MBs) instead of fluorophores. In this chapter, we explore the evolution of the automation of whole cell detection and enumeration that led to the development of microcytometers and particularly examine the anatomy of magnetic microcytometers applied to cancer research. We then give an overview of the challenges of Circulating Tumor Cells enrichment and enumeration, and the progress of magnetic microcytometers in this field.