The expression of alpha (alphaA and alphaB) and beta (betaA1/A3, betaA2, betaA4, and betaB2) crystallin genes were analyzed at the mRNA and protein levels in rat retinas with ocular hypertension-induced ganglion cell death. An animal model with progressive loss of retinal ganglion cells (RGC) was generated by elevation of intraocular pressure (IOP). The estimated RGC loss was approximately 8% and 20% at 2 and 5 weeks post IOP elevation, respectively. mRNA and protein quantification showed that alpha and beta crystallin genes were downregulated at both transcriptional (alphaA, alphaB, betaA1/A3, betaA4, and betaB2 approximately 50% and betaA2~40%) and protein (alphaA~50%, alphaB~63%, betaA1/A3~70%, and betaB2~38%) levels 2 weeks after IOP elevation. In experimental retinas 5 weeks after IOP elevation, the levels of crystallin mRNAs were higher than at 2 weeks and were comparable to that of control retinas. However, the levels of the corresponding proteins were still lower (alphaA, alphaB, and betaB2 approximately 37% and betaA1/A3~70%) than in control retinas. Furthermore, we found that the expression of these genes in the retina is predominantly localized to the cells in the GCL and to a lesser degree in the INL and ONL. Colocalization of the crystallin-positive and Fluorogold retrogradely labeled cells indicated that the cells expressing alpha and beta crystallins in the GCL are RGCs. In summary, we showed that alpha and beta crystallins are expressed in the retina predominantly by RGCs and that their expression is affected by ocular hypertension.