The objective of the research work was to formulate, optimize and evaluate the omeprazole loaded enteric coated microspheres. Microspheres were successfully prepared by orifice-ionic gelation process and optimized by using 32 full factorial design using two independent variables (concentration of sodium alginate and stirring speed) and three dependent variables (in vitro drug release, encapsulation efficiency and in vitro mucoadhesion). The effect of all variables was assessed by surface response methodology. The prepared formulations were evaluated in terms of micromeritic properties, percentage yield, particle size, in vitro drug release, encapsulation efficiency, zeta potential and in vitro mucoadhesion. Based on response surface methodology, the F6 formulation was considered as best with an entrapment efficiency of 85.45%, mucoadhesion of 91.04% and in vitro drug release of 55.39% in12 hrs. The stability study indicated that none of the formulation showed significant changes in percent residual drug content. The present study reports the successful preparation of omeprazole loaded enteric coated microspheres for effective prolongation of the duration of action and it also protects the drug from the acidic environment of stomach, thus increasing the therapeutic outcome.