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Background Retinal ganglion cell (RGC) death from ischemia reperfusion injury and optic nerve transection are challenges to successful restoration of vision by whole eye transplantation (WET). We examined whether University of Wisconsin Solution (UW) or a modified version which includes valproic acid and BaCl2 (mUW) can preserve RGCs in a WET model. Methods 24 hemifacial rat flaps prepared for WET were flushed with heparinized saline, UW, or mUW. After 85 minutes of ischemia, donor eyes were injected with the same solutions and prepared for immunohistochemistry (IHC) analysis before (n=6/group) or POD7 after (n=3/group) syngeneic WET. Donor and untreated non-ischemic naïve (n=4) retinas were stained for Brn3a and p-cJun (PNJ) to assess RGC viability and apoptosis respectively. Results After 85 minutes of ischemia, all donor eyes across treatments (saline, UW, or mUW), had equal levels of Brn3a+ and PNJ+ expression (P>0.05). Naïve eyes averaged ~100k Brn3a+ and ~18k PNJ+ RGCs. At POD7, saline and UW donor eyes each had ~20% loss in Brn3a+ RGCs as compared to control naïve eyes (P<0.05). At POD7, apoptotic signaling increased in both UW and saline donor eye, doubling in PNJ+ signal compared to non-ischemic naïve eyes (P<0.05). Conclusions Using a novel system to asses RGC degradation and apoptosis in an experimental rodent WET model, we found that UW and mUW solutions as formulated did not preserve RGCs after WET, despite reports of their anti-ischemic properties in other studies.