I never eat food heated / cooked in a microwave oven - we do not have one at home. Even while traveling, I would rather go hungry than eat food which needs to be cooked / reheated in a microwave.
The reason is simple. It heats the food from "inside out" by tampering with the molecular structure of the food. The "prana pattern" of the food gets vitiated. Understanding things in that paradigm is good enough for me. But the scientific types, they need scientific explanations. Just came across an answer in Quora which addresses the question from that angle, which I am appending below.
For the ultra scientific types who would like to dig out studies that prove the exact opposite, there will be many articles (no doubt promoted by the Devil's Own food lobby) that will prove the exact opposite, that microwaving food is perfectly fine, to them I would say "don't bother" - since I would then go back to my reasons for avoiding microwaved food and be quite smug and happy in my beliefs :-)))
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(From a Quora Answer by Rahul Srivastava. )
This is how microwave ovens work. Microwaves in microwave oven heat food by making the water molecules in the food vibrate at very high frequencies. Water molecules get torn apart and their structure changes. The heated water in turn heats the food. When this happens, the food's chemical structure changes. This differs from conventional heating of food, where heat is transferred by convection inward from outside.
And because of the way microwave heats food, microwaving produces radiolytic compounds, which are compounds neither found in humans nor in nature. It is not yet known what effects radiolytic compounds have on human body. Since these compounds are not natural, I wonder if their effects are beneficial or even harmless.
Also, carcinogenic toxins can leach out of plastic and paper containers into the food that is being microwaved. No matter how foolproof your microwave oven is, there is leakage of microwave. Although the leakage of microwave from microwave ovens may be very small, exposure over a long period of time should surely causes some damage to human body. The leakage from microwave oven worsens as it gets older.
Microwaving food also negatively alters its nutritional value. For example, a study showed that one minute of microwaving inactivates allinase in garlic, which is known for its anti-cancer benefits. Another study found that heating milk for about five minutes in a microwave oven reduces the B12 content to nearly half.
Research by Russian scientists in 1970s found that: microwaving of milk and grains converted some of the amino acids into carcinogenic substances; microwaving prepared meats caused the formation of the cancer-causing agents d-Nitrosodienthanolamines; thawing frozen fruits by microwave converted their glucoside and galactoside fractions into carcinogenic substances; microwaving frozen vegetables converted their plant alkaloids into carcinogens etc.
A Swiss food scientist concluded in a study that due to consumption of food prepared by microwave cooking, changes took place in the blood that could cause negative health effects such as increased cholesterol levels; decreased numbers of leukocytes (white blood cells) and red blood cells; production of radiolytic compounds etc.