Angiogenesis is a complex process that can be regarded as a series of sequential events comprising a variety of tissue cells. The major problem when studying angiogenesis in vitro is the lack of a model system mimicking the various aspects of the process in vivo. In this study we have used two in vitro models, each representing different and distinct aspects of angiogenesis. Differentially expressed genes in the two culture forms were identified using the suppression subtractive hybridization technique to prepare subtracted cDNA libraries. This was followed by a differential hybridization screen to pick up overexpressed clones. Using comparative multiplex RT-PCR we confirmed the differential expression and showed differences up to 14-fold. We identified a broad range of genes already known to play an important role during angiogenesis like Flt1 or TIE2. Furthermore several known genes are put into the context of endothelial cell differentiation, which up to now have not been described as being relevant to angiogenesis, like NrCAM, Claudin14, BMP-6, PEA-15 and PINCH. With ADAMTS4 and hADAMTS1/METH-1 we further extended the set of matrix metalloproteases expressed and regulated by endothelial cells.Keywords: differential gene expression; MVEC; angiogenesis; suppression subtractive hybridization.Angiogenesis, the formation of new capillaries from preexisting blood vessels, plays a crucial role in a wide range of normal and pathological processes, and is necessary for the continous growth of solid tumors [1,2]. Angiogenesis takes not place in a single step, but is a complex sequential process that relies on a controled cross-talk between endothelial cells and the surrounding avascular environment [2,3]. Upon activation by growth factors or cytokines, endothelial cells start to degrade the surrounding extracellular matrix and invade the avascular tissue. The tight endothelial cell-cell adhesion is disrupted, the cells start to proliferate and migrate into the avascular environment. Finally they stop proliferating and differentiate to tubular structures (reviewed in [3]). Most recent studies have focused on the effect of specific growth factors and cytokines secreted by non endothelial cells on angiogenesis, but little is known about the sequential events taking place in the activated endothelial cells during the formation of new blood vessels.In this work we chose a model system where human microvascular endothelial cells (MVEC) are cultured on a gel composed of extracted basement membrane derived from mouse Engelbreth±Holm±Swarm sarcoma (matrigel) [4]. When seeded at a certain density the cells stop proliferating and virtually all cells are induced rapidly to form capillary-like, lumen containing structures [4,5]. These cells were compared against nondifferentiating, proliferating MVEC again representing an important step during the formation of new blood vessels [2,3]. The advantage of these culture systems is that they can be performed with one and the same cell type resulting in two different homogenous populatio...