Recent Genome-wide Association Studies (GWASs) for eye diseases/traits have delivered a number of novel findings across a diverse range of diseases, including age-related macular degeneration (AMD), glaucoma and refractive error. However, despite this astonishing rate of success, the major challenge still remains to not only confirm that the genes implicated in these studies are truly the genes conferring protection from or risk of disease but also to define the functional roles these genes play in disease. Ongoing evidence is accumulating that the single nucleotide polymorphisms (SNPs) used in GWAS and fine mapping studies have causal effects through their influence on gene expression rather than affecting protein function. The biological interpretation of SNP regulatory effects for a tissue requires knowledge of the transcriptome for that tissue. We summarize the reasons to characterize the complete retinal transcriptome as well as the evidence to include an assessment of differences in regional retinal expression.