A pectin-based colon specific delivery system bearing 5-fluorouracil (5-FU) was developed for effective delivery of drug to the colon. Calcium pectinate gel (CPG) beads were prepared by ionotropic gelation method followed by enteric coating with Eudragit S-100. The CPG beads formed were spherical with smooth surfaces. CPG beads size was found to be in the range of 1.32 +/- 0.12 - 1.88 +/- 0.08mm. The in vitro drug release was investigated using USP dissolution rate test paddle type apparatus in different simulated mediums. Release in PBS ( pH 7.4) and simulated gastric fluid showed almost similar pattern and rate, whereas a significant increase in percent cumulative drug release ( 58.3 +/- 1.36%) was observed in medium containing rat caecal content, i.e. the amount of the drug released from the formulation was found to be 49.2 +/- 2.29 and 58.3 +/- 1.36% of drug with 2 and 4% w/ v caecal matter after 24 h whereas in control study 33.2 +/- 1.19% of drug was released. Moreover, to induce the enzymes that specifically act on pectin, the rats were treated with 1ml of 1% w/ v dispersion of pectin for 2 and 4 days and release rate studies were repeated in SCF in the presence of 2 and 4% w/ v of caecal matter. A marked improvement in the drug release was observed in presence of caecal matter obtained after induction when compared to those without induction. The percentage of drug released after 24 h release was observed to be 69.3 +/- 2.81 and 86.7 +/- 3.15%, respectively, with 2 and 4% w/ v rat caecal matter obtained after 2 days of enzyme induction, and 82.4 +/- 3.15 and 98.7 +/- 4.26%, respectively, after 4 days of enzyme induction. In vivo data showed that Eudragit S-100 coated calcium pectinate beads delivered most of its drug load ( 93.2 +/- 3.67%) to the colon after 9 h, which reflects its targeting potential to the colon. It is concluded that orally- ssadministered 5- FU loaded Eudragit S- 100 coated calcium pectinate beads can be used effectively for the specific delivery of drug to the colon.