Flow cytometry is an advanced group of techniques for counting and quantifying microscopic particles such as cells, chromosomes, or functionalized beads. These approaches employ sophisticated optical and fluidic components to detect scattered light and fluorescent signals from cells as they sequentially pass an interrogation point. Cytometry plays a crucial role in the diagnosis of immunological disorders and cancers, and is a mainstay technique in basic research settings such as hematology, cell biology, and biomolecular screening. However, in spite of the breadth of applications spanning many fields, flow cytometry in neuroscience has been largely unexploited and has seen only a steady increase in interest until recent years. This is rather surprising as the potential of flow cytometry in neuroscience applications was recognized in the early 1980s as the technology was evolving.