Purpose: To investigate the role of vascular endothelial growth factor-A (VEGF-A) isoforms in neovascular age-related macular degeneration. Methods: Choroidal neovascular membranes (CNV) were excised in 24 patients, 8 of them underwent previous photodynamic therapy. All procedures were performed before anti-VEGF therapies were implemented in Germany. Normal human donor eyes served as controls. Messenger RNA expression of total VEGF-A and VEGF-A isoforms was measured. Results: Vascular endothelial growth factor-A 121 is the most abundant isoform in CNV and control tissues. In controls, VEGF-A 121 is lowest in neural retina and highest in choroids. For total VEGF-A and VEGF-A 165, this is vice versa. VEGF-A 165 and VEGF-A 189 are significantly higher in CNV than in control choroids, the opposite is found for VEGF-A 121. After photodynamic therapy, total VEGF-A and VEGF-A 121 are increased, VEGF-A 165 and VEGF-A 189 are decreased. Age-dependently, there is an increase in VEGF-A 165 and a decrease in VEGF-A 121. Conclusion: Vascular endothelial growth factor-A isoforms are differentially distributed, suggesting that tissue-specific regulation of various isoforms is physiologically important. The disruption of this homeostasis in CNV membranes may be significant in the onset and progression of neovascular age-related macular degeneration. Our findings support the dominant role of VEGF-A 121 in neovascular age-related macular degeneration but hint that VEGF-A 165 may have an equivalent role in other neovascular retinal pathology.