CFSE (Carboxyfluorescein succinimidyl ester) is a fluorescent cell staining dye. CFSE is commonly confused with CFDA-SE, although they are not strictly the same molecule; CFDA-SE is cell permeable, while CFSE is not. As CFDA-SE enters the cell cytoplasm, intracellular esterases convert the molecule to the flourescent ester, CFSE, which is retained within cells.

CFSE is a simple and sensitive technique for analysis of multiple parameters of cells. This method allows us to examine specific populations of proliferating cells and identify 7–10 successive cell generations. CFSE consists of a fluorescent molecule containing a succinimydyl ester functional group and two acetate moieties. CFSE diffuses freely inside the cells and intracellular esterases cleave the acetate groups converting it to a fluorescent, membrane impermeable dye. This dye is not transferred to adjacent cells. CFSE is retained by the cell in the cytoplasm and does not adversely affect cellular function. During each round of cell division, relative fluorescence intensity of the dye is decreased by half. In addition, unlike other methods, CFSE-labeled viable cells can be recovered for further analysis.

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