This invention relates to the preparation and evaluation of novel targeted drug delivery of metronidazole to the colon. The present method includes preformulation studies of drug and carrier system which includes organoleptic properties, identification, saturation solubility, partition co-efficient and FTIR studies of metronidazole. Preparation and characterization of metronidazole- β-cyclodextrin inclusion complex. Formulation and optimization of eudragit S100 coated metronidazole granules and formulation and evaluation mucopenetrating nanoparticles of Eudragit S100 coated metronidazole chitosan HPMCP nanoparticles.