Porous polymer monolith have been prepared in capillaries with circular or square cross section and lateral dimensions of 50, 75, 100 μm as well as in a rectangular 38 × 95 μm capillary. These capillaries have been used to determine the effect of the size and shape of their cross section on the porous and hydrodynamic properties of poly(butyl methacrylate-co-ethylene dimethacrylate) monoliths. The capillaries were studied by scanning electron micrography and evaluated for their permeability to flow and their performance in the liquid chromatographic separation of a protein mixture comprising ribonuclease A, cytochrome c, myoglobin, and ovalbumin using a linear gradient of acetonitrile in the mobile phase. No differences resulting from channel geometry were found for the various capillary columns. These results demonstrate that standard capillaries with circular geometry are a good and affordable alternative conduit for modeling the processes carried out in microfluidic chips with a variety of geometries.