Consumption of wholegrain foods has been recommended for healthy diets. The beneficial health properties of wholegrain products have been associated with the presence of higher amounts of dietary fiber and antioxidants and lower calories as compared to their respective refined ones. Phenolic compounds are mainly attributed to antioxidant properties of wholegrain foods. This review article provides a single comprehensive source that describes effects of milling and thermal processing on phenolic compounds and antioxidant properties in cereals. In general, milling and pearling processes affect the distribution of phenolic, compounds and thus antioxidant properties vary among the milling fractions. Thermal processes such as baking and extrusion could cause negative or positive effects on phenolic compounds and antioxidant properties of the end product subject to grain type and processing conditions. Thus factors that enhance health benefits of wholegrain cereal products have been discussed.