Many cell populations have been labeled using stable reporters containing a fluorescent protein. These same marker lines can be used to capture specific cell types or marked cell populations after a brief enzymatic digestion to dissociate tissues. Here, we describe the use of Fluorescence Activated Cell Sorting (FACS) to isolate a rare population of cells marked with Green Fluorescent Protein (GFP). The FACS is a powerful selection tool that can be used to isolate high-quality RNA while selecting for fluorescence, cell size, and other properties.