Objective To formulate and evaluate Albendazole microcapsules using chitosan, a natural polymer for colon-specific delivery for better treatment of helminthiasis, filariasis, colorectal cancer, avoiding the side effects. Methods The Albendazole microcapsules were prepared by the use of different concentrations of sodium alginate, chitosan and hydroxypropyl methylcellulose (HPMC). The polysaccharides chitosan reacted with sodium alginate in the presence of calcium chloride to form microcapsules with a polyelectrolyte complex membrane by electrostatic interactions between the two oppositely charged polymers. The microcapsules were then studied for entrapment efficiency, drug-polymer compatibility and surface morphology. In vitro drug release study in presence and absence of cecal content were also studied. Further, kinetic modellings were employed to find out release mechanisms. Results Albendazole loaded microspheres showd high entrapment efficiency (72.8%) and the microcapsules were free flowing, non aggregated and spherical, between 600 and 1000 μm in diameter. The surface of microcapsules were found to be porous and wavy. The FT-IR spectrum showed that there is no interaction between the polymer and the drug. The in vitro drug release study found to be affected by change in chitosan, sodium alginate and HPMC concentration. The microcapsules with 2.5% sodium alginate and 0.4% chitosan shown minimum release in gastrointestinal simulated condition but shows maximum drug release at the end of 24th hour in presence of cecal content. The rate of drug release follows Korsmeyer-peppas model that was the drug release is by diffusion and erosion. Conclusions The study reveals that Albendazole loaded chitosan-alginate based microsphere can be used effectively for the colon targeting.