Variants of the green fluorescence protein (GFP) are useful tools in many biological research applications. Two of the GFP spectral variants, the cyan and yellow fluorescence proteins (CFP and YFP), have compatible excitation and emission properties as fluorescence donor and acceptor in fluorescence resonance energy transfer (FRET). A protocol is described here to study the molecular association between p80 TNFR-2 and TRAF2 fusion proteins containing CFP and YFP using flow cytometric FRET measurement. The utility of this application in the study of protein-protein interaction is discussed.