Flow cytometry allows the rapid measurement of structural features of thousands of single cells while they move through a focused light source. Specific fluorescent labeling of proteins or structures in the cell is required for many flow cytometry applications. The fluorescent labeling of SNAP-tag fusion proteins in cells provides a rapid new approach to satisfy this need. The SNAP-tag is a protein tag that labels itself with fluorophores or other substituted groups presented as a benzyl guanine-based substrate. This reaction is highly specific and robust in a wide range of reaction conditions, and no other protein reacts with this class of substances. SNAP-cell substrates are cell permeable and can therefore be used to label SNAP-tag fusion proteins inside live cells. SNAP-vitro substrates are highly soluble, charged substrates which are not cell permeable but ideally suited for specific labeling of cell-surface exposed SNAP-tag fusion proteins. This application note describes the use of SNAP-cell and SNAP-vitro substrates to label SNAP-tag fusion proteins in living cells followed by fixation with 1% paraformaldehyde (PFA) or 70% ethanol and analysis using flow cytometry. Results for CHO-K1 cells transiently expressing SNAP-NK1-R, a SNAP-tag G-protein coupled receptor (GPCR) fusion protein, or expressing SNAP-H2B, a SNAP-tag Histone 2B fusion protein are presented. The spectral characteristics of the substrates used are shown in Table 1.