Background: Different methods have been studied for targeting drugs to the colon, such as pH-based, time dependent and bacterially degradable systems. However, due to variations in physiological conditions of patients, one system alone could not be completely reliable on colonic drug delivery. Objectives: The aim of this study was preparation and evaluation of a novel colon-specific drug delivery system for 5-ASA (mesalazine) pellets using pectin as a microbially degradable polymeric carrier and Eudragit RS (ERS) and Eudragit RL (ERL) as time-dependent polymers. Materials and Methods: Formulations were constructed based on a multilevel full factorial design. Pellets were prepared via extrusion - spheronization and evaluated for physicochemical properties, image analysis, SEM, FT-IR, DSC and in vitro drug release studies in the simulated gastric fluid with pH = 1.2 (SGF), simulated intestinal fluid with pH = 6.8 (SIF) and simulated colonic fluid with pH = 6.8 in presence of pectinolytic enzyme (SCF). Results: It was shown that in the presence of pectin, formulations without ERL had a relative resistance to drug release in SGF. Pellets containing pectin and the least amount of ERS had the highest burst release effect in SCF. On the other hand, increasing in amount of ERS in the formulations caused a sustained drug release. Presence of pectin in formulations containing ERS and ERL caused sensitivity of formulations to pectinolytic enzyme which can suitable for a colon specific drug delivery system. Conclusions: It was shown that combination of pectin and eudragits can relatively control drug release in the upper GI. On the other hand, pectin degraded in the presence of pectinase and formulations were susceptible to the colonic media.