The present study aims to prepare and evaluate carbon nanotubes (CNTs)-based colon-specific microspheres using irinotecan as a model of drug. The synthesis of CNTs-based microspheres including attachment of folate-chitosan conjugate and irinotecan to CNTs via non-covalent interaction, followed by microencapsulation with Eudragit S-100 by an oil-in-oil solvent evaporation technique. The obtained samples were characterized in case of surface morphology, drug loading efficiency and particle size. In vitro drug release behavior was studied in different pH medium and the obtained data were subjected to kinetic equations. It was found that the Eudragit-coated microparticles were spherical with smooth surface, and the particle size varied with the core/coat ratio. In vitro drug release shows that the irinotecan released in a slow and sustained fashion from the CNTs-based carriers without coating with Eudragit. No drug release was observed from Eudragit-coated microspheres when the medium pH below 7, while when the pH reached 7.4, the coating layer of Eudragit began to dissolve and a controlled release of irinotecan was observed. The cell viability test indicates that the drug free FA-CS decorated CNTs had no influence on the cell proliferation rates of HT-29 cells, while the irinotecan-loaded CNTs drug system proved to be the most cytotoxic.