Quantification of retinal ganglion cell (RGC) loss/survival following a defined insult to the retina is a prerequisite in order to allow a comparison to be made between the effectiveness of potential neuroprotective drugs. The purpose of the present study was to extend the characterisation of our previously published semiquantitative RT-PCR assay to assess RGC loss/survival. Comparisons were made between the total mRNA levels of the ganglion cell-specific markers Thy-1 and neurofilament light (NF-L) in the retina at specific times after an intravitreal injection of N-methyl-D-aspartate (NMDA) or kainate or after 45 min of ischemia/reperfusion and also between the levels of NF-L mRNA and protein at various times after NMDA injection. Changes in Thy-1 and NF-L immunoreactivities were also observed. NMDA, kainate and ischemia/reperfusion all caused a reduction in the retinal content of Thy-1 and NF-L mRNAs and immunoreactivities. An excellent correlation was observed between the levels of the two mRNAs after these treatments. After NMDA, loss of NF-L mRNA was shown to precede loss of NF-L protein but total loss of each marker was similar after 7 days. The results of the study demonstrate that injury and subsequent death of RGCs, which occurs after ischemia/reperfusion and after intraocular injection of NMDA or kainate, can be followed by measurement of total retinal levels of Thy-1 and NF-L mRNAs and NF-L protein. The assays provides accurate, practical and complementary methods for assessing the potential benefits of neuroprotective drugs on RGCs which have been injured by a variety of experimental modalities.