The interaction of the cell surface proteins plays a key role in the process of transmembrane signaling. Receptor clustering and changes in their conformation are often essential factors in the final outcome of ligand receptor interactions. Fluorescence resonance energy transfer (FRET) is an excellent tool for determining distance relationships and supramolecular organization of cell surface molecules. This paper reviews the theoretical background of fluorescence resonance energy transfer, its flow cytometric and microscopic applications (including the intensity based and photobleaching versions), and provides a critical evaluation of the methods as well. In order to illustrate the applicability of the method, we summarize a few biological results: clustering of lectin receptors, cell surface distribution of hematopoietic cluster of differentiation (CD) molecules, and that of the receptor tyrosine kinases, conformational changes of Major Histocompatibility Complex (MHC) I molecules upon membrane potential change and ligand binding.