Abstract Water based polymer systems are often used for improvement in the properties of plain cement mortar or concrete. Presently, latexes of a single or combinations of polymers like polyvinyl acetate, copolymers of vinyl acetate–ethylene, styrene–butadiene, styrene–acrylic, and acrylic and styrene butadiene rubber emulsions are generally used. One of the limitations of these polymer systems is that they may re-emulsify in humid alkaline conditions. To overcome this problem, an epoxy emulsion based polymer system has been developed. In this paper the properties of the cement mortar modified with this newly developed epoxy emulsion are compared with those of the acrylic-modified mortar. The results showed that the mortars with the newly developed system have superior strength properties and better resistance to the penetration of chloride ions and carbon dioxide.