Ordered mesoporous carbons that encapsulate the poorly soluble compounds ibuprofen and indomethacin were systematically studied by means of X-ray diffraction (XRD), differential scanning calorimetry (DSC) and X-ray photon electron spectroscopy (XPS). The results showed marked differences in the release profiles of the two drug molecules in simulated gastric fluids. In vitro toxicity profiles appear to be compatible with potential therapeutic applications bringing them to the forefront as carriers of poorly water soluble drugs.