Pantoprazole is a prodrug used in the treatment of acid related disorders and Helicobacter pylori infections. It is activated inside gastric parietal cells binding irreversibly to the H(+)/K(+)-ATPase. In this way, pantoprazole must be absorbed intact in the intestinal tract, which indicates that enteric drug delivery systems are required for its oral administration. The purpose of this study was to investigate the physical characteristics of enteric pantoprazole-loaded microparticles prepared by spray drying using a blend of Eudragit S100 and HPMC. The microparticles were produced in different spray dryers and operational conditions at laboratory and pilot scales. Microparticles produced with two fluid nozzle atomizer and air pressure of 196 kPa presented satisfactory encapsulation efficiency and gastro-resistance. Microparticles produced with the same atomizer but using 49 kPa of air pressure presented strings in the powder. The microparticles produced in mixed flow presented very high polydispersity and the ones produced with rotating disc atomizer presented drug crystals adsorbed on the particle surfaces. The microparticles produced with two fluid nozzle atomizer and 196 kPa were prepared in three consecutive days for the process validation. The powders showed reproducible diameter, polydispersity, densities, encapsulation efficiency and gastro-resistance profile.