Purpose Diabetic retinopathy is one of the worst complications of diabetes and can threaten sight. The aim of our study is to compare the clinical outcomes and ultrastructural changes in diabetic retinopathy patients after intravitreal admission of either ranibizumab ( Lucentis) or aflibercept (Eylea). Methods In our prospective study, 27 patients with PDR were enrolled. They were divided into two groups - 14 PDR patients treated with ranibizumab and 13 PDR patients treated with aflibercept. In both groups, a complete ophthalmological examination was performed, including OCT. In 12 patients (6 from each group), pars plana vitrectomy was performed with excision of epiretinal membranes. Transmission and scanning electron microscopy of the membranes was performed. Results Clinical findings - in both groups there was a decrease in the neovascular proliferation and macular oedema. CRT was reduced with approximately 100-120 mk. In the Eylea group, there was general shrinking of neovascular proliferation with lower risk of bleeding. The ultrastructural analysis showed more significant reduction in endothelial fenestration after Eylea application, with clustering of platelets and erythrocytes in the capillary lumen. Increased numbers of macrophages were found in the membranes of both groups. Conclusion Our results show that aflibercept is very effective in treating PDR. It causes more significant reduction of endothelial fenestration and more evident thrombotic microangiopathy than other anti-VEGF drugs, and thus diminishes macular oedema and prevents neovascular tissue from bleeding. Eylea inhibits both VEGF and placental growth factor and thus modifies the whole pathophysiology of DR. It is therefore more effective than other treatment medications.