Formation of both health promoting and potential harmful substances (acrylamide and hydroxymethylfurfural) has been associated to the extent of the Maillard reaction. The effects of recipe compositions in terms of leavening agent (ammonium and sodium bicarbonates) and sugars (sucrose and glucose), and baking conditions (temperature and time) on the antioxidant activity (AOA) in cookies were studied. The cookies were baked at different temperatures (180-220 degrees C) for different times (10-25 min). AOA was measured by the ferric reducing power (FRAP), 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,2,-diphenyl-1-picrylhydrazyl (DPPH) coloured radicals, and oxygen radical absorbance capacity (ORAC-fluorescein) in automated plate-reader assays. Net AOA varied regarding the assay applied, whereas higher AOA was always obtained for the ABTS assay and lower for DPPH assay, and ranging from 2 to 200 mu mol Trolox/g sample. At higher temperature and baking times, higher AOA in cookies regardless of the formulation was recorded. Glucose enhances formation of compounds with higher AOA compounds as compared with sucrose recipes. Ammonium bicarbonate clearly promotes the formation of AOA for sucrose recipes but this effect is not observed in glucose recipes and varied with the AOA procedure applied. A risk/benefit index, based on the concomitant formation of neo-formed contaminants and substances with AOA (potentially health-promoting substances) is presented, and its application for recipe comparison is discussed. Risk/benefit index rapidly increased with increased temperature and time of baking.