The present study was to develop oral mucoadhesive drug delivery systems of metronidazole for an effective and safe treatment of Entamoeba histolytica. The microspheres were formulated by orifice-ionic gelation technique using chitosan, Sodium alginate and Sodium carboxymethyl cellulose in different concentrations. The resultant microspheres were evaluated for different in vitro and in-vivo evaluation parameters. In in-vitro studies, it was observed that increased concentration of Chitosan had a positive effect on the encapsulation of all drugs. The particle size increased with increasing of drug-polymer ratio. Bioadhesion was influenced with increase in pH and it was more rapid in intestine, rather than in stomach. The drug-polymer interaction was also studied by conducting FTIR and DSC tests. To assess the stability of all formulations for two years, the short term stability studies of the selected batches were carried out by keeping them at 40°C ± 2°C and 75% ± 5% RH for a period of six months.