Cell-cell fusion is an important biological and pathological event. There are limited techniques for studying both the process of cell-cell fusion and the fate of fused cells. We have developed a non-invasive assay for the temporal analysis of cell-cell fusion, quantification of fused cells, and isolation of fused cells. Briefly, cells are transfected with either the T7 bacteriophage RNA polymerase, or yellow fluorescent protein (YFP) driven by a T7 specific promoter. Cells are mixed and induced to fuse. When cells expressing T7 RNA polymerase and T7 promoter driven YFP (T7-YFP) fuse and the cellular contents mix, the YFP is expressed. These YFP-positive cells can be detected with a fluorescent microscope, quantified by flow cytometry, or collected using fluorescence associated cell sorting. Isolated YFP-positive cells can be monitored to determine the fate of fused cells, specifically for the rates of growth, transformation, and changes in chromosome number.