The rapid development in combinatorial chemistry of millions of novel potential drug candidates requires in vitro devices for reliable testing of their transendothelial transport and the uptake in specific cells. To date, this is often achieved in vitro by the use of regular planar Boyden chambers, which are not reflecting the three dimensionality of the blood vessel. This technical note describes the fabrication and biological validation of a novel three-dimensional Boyden chamber system for studying transendothelial transport. The key element of this new system is a porous thin-walled microchannel produced by a SMART (substrate modification and replication by thermoforming) process comprising a combination of microthermoforming and ion track technology. The membrane-like microstructure offers the opportunity to grow endothelial cells on the inner side of the channel resembling a more natural curved organization of vessels. After establishment of a confluent HUVECs layer in the porous microchannel this novel Boyden chamber was successfully applied to study the transendothelial transport of a polycationic cell penetrating peptoid through the 3D- or curved endothelial cell layer. Thus, this system will enable the investigation of such synthetic compounds as drug delivery systems with regard to their bioavailability and functionality under organotypic conditions.