In order to develop novel therapies for the treatment of central nervous system diseases, methods for rapid quantification of different neural cell populations, from healthy or diseased brains, are highly desirable. Today, the method of choice to quantify different cell populations in the brain is immunohistochemistry. This technique is precise and reliable, but is also very time consuming and cost-intensive. In this paper, we describe a rapid procedure where neurons and neural stem/progenitor cells from the adult mouse are isolated, immediately fixed, and quantified with different cell type specific markers by flow cytometry. Our results show that we can reproducibly detect and quantify mature neurons with antibodies towards microtubuli associated protein (MAP2) and neuronal nuclei (NeuN), both in hippocampus and olfactory bulb. Stem/progenitor cell detection and quantification were achieved using antibodies specific for bromodeoxyuridine (BrdU) and doublecortin (DCX). The flow cytometric analysis revealed fractions of positive cells corresponding to the in vivo situation, confirmed and validated by traditional immunohistochemistry and stereological counting procedures. We conclude that the flow cytometric technique can be used as a rapid screening method to accurately quantify neuronal populations and to detect and quantify other brain cell types, such as neural stem/progenitor cells.