In the renal cortex the peri-tubular capillary network and the proximal tubular epithelium co-operate in solute and water reabsorption, secretion, and inflammation. However, the mechanisms by which these two cell types co-ordinate such diverse functions remain to be characterized. Here we investigated the influence of microvascular endothelial cells on proximal tubule cells using a filter based, non-contact, close proximity co-culture of the human microvascular endothelial cell line, HMEC-1 and the human proximal tubular epithelial cell line, HK-2. Using DNA microarrays the transcriptome of HK-2 cells cultured in mono or co-culture was compared. HK-2 cells in co-culture exhibited a differential expression of 114 genes involved in pathways such as extracellular matrix (e.g. lysyl oxidase), cell-cell communication (e.g. IL-6 and IL-1beta) and transport (e.g. GLUT3 and lipocalin 2). HK-2 cells also exhibited an enhanced paracellular gating function in co-culture, which was dependent on HMEC-1 derived extracellular matrix. We identified a number of HMEC-1 enriched genes which are potential regulators of epithelial cell function such as extracellular matrix proteins (e.g. collagen I, III, IV and V, laminin alpha IV) and cytokines/growth factors (e.g. HGF, endothelin 1, VEGFC). This study demonstrates a complex network of communication between microvascular endothelial cells and proximal tubular epithelial cells which ultimately effect proximal tubular cell function. This co-culture model and the data described will be important in the further elucidation of microvascular endothelial and proximal tubular epithelial cross talk mechanisms.