The physical association of HLA class I and class II Ag in the membranes of PGF and JY lymphoblastoid cell lines was studied using flow cytometric energy transfer. This technique measures the proximity of cell surface molecules in the nm range and provides a distribution histogram of the average proximity of molecules on each cell of a population. HLA Ag were labeled with mAb conjugated to fluorescein, serving as donor, or tetramethylrhodamine, serving as acceptor molecules. Significant fluorescence energy transfer was detected between various combinations of class I and class II molecules indicating that these molecules are within 10 nanometers of each other. Specifically, energy transfer was observed between class I molecules and DR, DQ, or DP class II HLA molecules. In addition, energy transfer between all combinations of DR, DQ, and DP molecules was observed. No transfer was observed among class I molecules or among DR or among DP molecules. Among DQ molecules, subpopulations transferred fluorescence energy to each other. The close contact measured between class I and class II Ag correlates with previous reports of cocapping and may reflect an immunologically significant interaction or the reported tendency of class I Ag to associate with other cell surface receptors, including growth factor receptors. The energy transfer between fluorescent antibodies to class II Ag suggests the existence of heterodimers formed from the different locus products, as well as possible quaternary surface interactions between alpha/beta complexes from separate loci.