The purpose of this study was to examine chitosan (CS)-carboxymethyl starch (CMS) nanoparticles as drug delivery system to the colon. The 5-aminosalicylic acid (5-ASA) was chosen as model drug molecule. CS-CMS nanoparticles were formulated by a complex coacervation process under mild conditions. The influence of process variables, including the two ionic polymers, on particle size, and nanoparticles entrapment of 5-ASA was studied. In vitro release of 5-ASA was also evaluated, and the integrity of 5-ASA in the release fraction was assessed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The release of 5-ASA from nanoparticle was based on the ion-exchange mechanism. The CS-CMS nanoparticles developed based on the modulation of ratio show promise as a system for controlled delivery of drug to the colon.