The morphological and functional differences between the retinal and choroidal vascular bed raise the question of whether the smallest functional unit, the microvascular endothelial cell (MVEC), also differs in its basal characteristics. Here, we examined bovine retinal and choroidal MVECs (rMVECs, cMVECs) for the presence and regulation of angiogenic mediators and their receptors, and cytokines at the mRNA level using quantitative RT-PCR and differential display. Vascular endothelial growth factor (VEGF) mRNA was expressed in both rMVECs and cMVECs. The basal and hypoxia-increased VEGF mRNA levels were significantly higher in cMVECs, which may indicate a higher capacity for autocrine stimulation in these cells. The mRNA for two VEGF receptors, Flt-1 and Flk-1, was present in rMVECs and cMVECs. Interestingly, rMVECs expressed higher Flt-1 but lower Flk-1 mRNA levels compared to cMVECs. Examining the angiopoietin (Ang)/Tie-2 system, we only detected Ang-1 mRNA at very low levels. While Ang-2 mRNA levels were high in both rMVECs and cMVECs, rMVECs expressed 2-3 times the basal and hypoxia-upregulated Ang-2 mRNA levels than did cMVECs. No difference was found in basal Tie-2 mRNA levels. rMVECs are the more potent producers of macrophage colony-stimulating factor (M-CSF) and granulocyte-macrophage CSF (GM-CSF), whereas cMVECs expressed higher RANTES mRNA levels. In our second approach - screening rMVECs and cMVECs for differentially expressed genes - we found liprin-beta1, calnexin, and sushi-repeat-containing protein, x chromosome (SRPX) mRNA in both MVEC types at varying levels. In summary, MVECs from the retinal and choroidal vascular beds showed quantitative differences in angiogenic regulator expression and in their capability to produce cytokines.