Properties of porous silicon which are relevant for use of the material as a stationary phase in liquid chromatography chips, like porosity, pore size and specific surface area, were determined with high-resolution SEM and N2 adsorption–desorption isotherms. For the anodization conditions investigated, porosity is between 20 and 60%, pore sizes between 2 and 5 nm and specific surface area between 130 and 410 m2/cm3. It was established that under identical anodization conditions, porous layer formation is 10–15% slower on micromachined pillars than on flat substrates, and depends on geometrical parameters like pillar diameter and height and interpillar spacing. In microchannels containing pillars with a porous silicon shell, chromatographic experiments on a coumarin dye mixture were performed, which in comparison with non-porous pillars showed a significant increase of the retention factors, resulting from the large internal surface of the porous pillars. The increased relative retention of one of the coumarin dyes, C480, could be correlated quantitatively with the measured internal surface of the porous layer. Due to the small pore size, these porous shell columns are particularly suitable for analytical or preparative separation of low-molecular weight molecules, with applications in metabolomics, food quality control, or medical diagnostics.