The simultaneous detection of the green fluorescent protein (GFP) and DNA content using propidium iodide (PI) by flow cytometry is made difficult because of the unique nature of these 2 fluorogenic reagents. For PI to enter cells efficiently and to stain DNA quantitatively, the cells must first be permeabilized; ethanol treatment is a routine method to achieve this. However, this permeabilization step causes GFP, which is normally found in the cytoplasm, to leach out of the cells. Although the use of paraformaldehyde-based fixatives allows GFP to be maintained in cells and retain its fluorescence even after ethanol permeabilization, the protocol we commonly employ results in inefficient PI staining and poor quality DNA histograms. To circumvent these difficulties, we have employed a GFP-fusion protein which localizes to the cellular membrane and as such is retained in cells upon ethanol permeabilization without prior fixation. This allows the GFP signal to be detected in cells treated with ethanol in preparation for PI staining and cell cycle analysis. This property facilitates the use of GFP as a marker for transfected cells in experiments designed to characterize the effects of ectopic expression of cellular or viral genes on cell cycle progression.