In order to understand the mechanisms of angioadaptation, information on gene expression in microvessels has become increasingly important. This study was designed to determine mRNA expression in microvessels and correlate them to different layers of wall crossection. mRNA from single segments (length ~5 mm) of arteries and veins in the rat mesentery (n=6) was amplified by real time duplex RT-PCR (dual-labeled probes). ß-actin served as an endothelial house keeping gene. Relative mass of endothelial cells (ec), smooth muscle cells (smc), and adventitia (adv) in vessel walls of arteries and veins was quantified by histometry on histochemically stained cross sections. Ratios of gene copy numbers relative to endothelial mass (a), given by ß-actin, and total wall mass (a * (ec/(ec+smc+adv))) for arteries and veins were determined. Per endothelial mass, gene expression values for Vegf (0.21±0.09/ 0.06±0.02) (arteries/ veins), Tie-2 (0.23±0.18/ 0.06±0.11), Vwf (0.3±0.18/ 0.72±0.27), Ang-2 (0.37±0.27/ 0.04±0.03) and Adamts-1 (0.35±0.32/ 0.59±0.65) were obtained. Relative to total wall mass, there is higher expression of Vwf and lower expression of Ang-2 respectively, in veins compared to arteries, whereas Vegf and Tie-2 exhibit similar expression values. The present approach maybe used to investigate molecular responses to environmental changes e.g. after vascular occlusion.