A variety of methods are used to process foods: if they are not edible, to render them so; to permit storage; to alter texture and flavor; to destroy microorganisms and other toxins. These methods include heating (baking, cooking, frying, microwaving), freezing, and high pH. It is a paradox of nature that the processing of foods can improve, nutrition, quality, and safety; yet, occasionally these processing alternatives can lead to the formation of anti-nutritional and toxic compounds. These multi-faceted consequences of food processing result from molecular interactions among nutrients and with other food ingredients, both natural and added. This paper outlines the following aspects of processing-induced formation of novel food ingredients and the resulting consequences for nutrition: protein-polyphenol and protein-carbohydrate enzymatic and non-enzymatic browning reactions; formation of heterocyclic amines in meat; inactivation of soybean inhibitors of digestive enzymes; formation of lysinoalanine and D-amino acids in food proteins; and the stability of phenolic compounds to high pH. Possible approaches to prevent the formation of deleterious food ingredients are also addressed.