There's a common misconception that microwaved food is bad for you, either because microwaving destroys nutrients or because the microwaves themselves somehow render the food unhealthy. While microwaving -- like all cooking methods -- does reduce the vitamin content of food to a small degree, evidence suggests that microwaving food may actually be healthier than cooking it conventionally.
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Microwave ovens cook food by emitting waves of energy that cause compounds -- specifically water molecules -- in your food to vibrate. The vibrating water molecules rub up against one another, which generates heat through friction. This process is analogous to that in which you feel your hands get warmer when you rub them together. Though common parlance associates microwaves with nuclear radiation -- microwaving food is sometimes referred to as "nuking" -- there's nothing nuclear about microwave technology.
Effect on Macronutrients
Microwaving your food doesn't affect the caloric content or healthfulness of the macronutrients -- proteins, carbohydrates, and fats -- in the slightest. All heating methods, microwaving included, denature proteins. Denaturation renders proteins functionless, but you don't depend upon the function of the proteins in the food you eat -- in fact, your stomach has the same denaturing effect. Denaturing proteins in no way reduces their nutritional value.
Effect on Micronutrients
Vitamins are sensitive micronutrients that your body cells need to remain healthy. Cooking reduces the vitamin content of your food to a small degree, explains Dr. D. Zhang and colleagues in a 2004 article in the scientific journal "Food Chemistry." Zhang notes that because all cooked food is lower in vitamin content than raw food -- this is particularly true of vegetables -- it's necessary to eat a little more of a cooked food than its raw counterpart to get the same nutritional benefit.
Benefits of Microwaving
In general, the vitamin content of a food decreases with increased cooking time. As such, food cooked for shorter periods of time -- regardless of the cooking method -- contains more of the original vitamins than food cooked longer. A 1994 study by Dr. M. Schnepf and colleagues in the "Journal of Food Quality" notes that microwaved vegetables actually maintain more vitamin content than conventionally cooked vegetables, because microwaves cook food to the same degree in a shorter period of time.