The present investigation was carried out to develop colon targeted drug delivery system which consists of chitosan-chondroitin sulphate interpolymer complex as a binder containing rifaximin in the core coated with Eudragit E-100 and Eudragit RL-100.The  chitosan-chondroitin sulphate interpolymer complex was characterized by Fourier Transform Infrared Spectroscopy. In vitro release studies of coated tablets were carried out for 2 h in pH1.2 HCl buffer, 3h in pH 7.4 phosphate buffer and 19 h in pH6.8 phosphate buffer in the presence and absence of rat caecal content. A drug release of 27.13% was observed with uncoated tablets in HCl buffer pH 1.2, 80.56% of drug release in phosphate buffer pH 7.4 and 99.23% was observed in phosphate buffer pH6.8. Also tablets coated with Eudragit E-100 and Eudradgit RL-100 with different coat weight showed less than 10% of drug release in the stomach whereas same tablets showed 23.22%, 15%, 13.39%, 12.83% release of drug in pH 7.4 phosphate buffer and 73.26%, 75.91%, 72.23%, 71.93% release of drug in pH 6.8 phosphate buffer. Histopathology of rat colon after administration of Eudragit E-100 and Eudradgit RL-100 coated tablets containing chitosan-chondroitin sulphate interpolymer complex revealed marked reduction in acetic acid induced colitis in test group.