We investigated the specificity of cyan fluorescent protein (CFP) expression in retinal ganglion cells (RGCs) of the transgenic Thy1-CFP (B6.Cg-Tg(Thy1-CFP)23Jrs/J) mouse line, and the characteristics of these cells after optic nerve injury. RGCs of adult Thy1-CFP mice were retrogradely labeled with fluorochrome (2% fluorogold [FG]) from the superior colliculi (SC). Animals were sacrificed 7 days after RGC labeling. Retinas were fixed and whole-mounted. CFP and FG-positive cells were visualized and imaged separately. Cells positive for CFP, FG, or co-labeled were counted. In another group of animals, the left optic nerves were transected 7 days after FG labeling. They were sacrificed 7 or 21 days after transection. The retinas were whole-mounted and the characteristics of CFP-expressing cells examined. CFP-expressing cells were distributed evenly throughout the retinas of Thy1-CFP mice. The average densities of CFP and FG-positive cells in the retina were 2778+/-216 and 3230+/-157 cells/mm(2), respectively. 93.2+/-1.6% of CFP-expressing cells were also labeled with FG. However, only 79.9+/-2.5% of FG-labeled RGCs expressed CFP. The number of CFP-expressing cells decreased dramatically after transection. Cells with spindle shape, immunohistochemically identified as microglia, were seen in the retina with CFP expression at both 7 and 21 days after optic nerve transection. In retinas of Thy1-CFP mice, CFP is expressed by the large majority of RGCs, but not exclusively by RGCs. CFP is internalized by phagocytosing cells after injury to RGCs.