I let my dishwasher sit unused for years because I ass-u-me-d that it was less efficient than hand-washing. Then one day I sat down to write a blog post about what a great person I am for hand-washing all my dishes even though I frickin’ hate doing it and the internet took me down a peg.* This led me to question many of the kitchen myths I had absorbed. Last year I looked into the very popular belief that there is a link between aluminum and Alzheimer’s disease and was thrilled to discover that there is none whatsoever.
The longtime use of microwaves at my family’s favorite natural foods co-op (the venerated “Hippy Connection”) was my sole basis for using a microwave oven in my own home for years. I couldn’t imagine them asking us to heat all our deli items with electromagnetic radiation if there was any doubt whatsoever as to its safety. The Hippy Connection works on the Precautionary Principle, a sort of guilty-until-proven innocent system for food and other products they sell, in which they vet everything before it crosses their threshold, getting proof of its wholesomeness, and any “natural,” “environmentally safe,” or other claims that it makes.
I encountered some extremely staunch resistance to microwave usage not too long ago and while the other party had no solid argument against I had no data for, either, so I decided to get some. Let’s fight anecdotes with data, shall we?
1) Microwave ovens are unsafe even to be around. Nope. Microwave ovens are regulated by the FDA. “Manufacturers must certify that their microwave ovens comply with strict FDA emission limits. The emission limits are well below the threshold for risk to public health.” Given your stance on government in general and the FDA in particular, this may not put you at ease, but it works for me. And unless your oven is physically damaged the waves can’t “leak”.
What about folks with pacemakers, you ask? “Today’s pacemakers are now designed to be shielded against electrical interference.”  Come to think of it, the last time I saw one of those little plastic “CAUTION: MICROWAVE IN USE” placards was more than ten years ago.
2) Microwaves zap the nutritional content of foods and/or make them otherwise unsafe to eat. Nuh uh. OK, I totally get how the “microwave radiation” thing sounds scary. It does! But keep in mind that radio waves are also electromagnetic radiation (they are shorter than radio waves, hence the “micro”) as is visible light. The “radiation” part is what’s scaring us, of course. But what you’re thinking of us nuclear radiation, not electromagnetic radiation. “Nuclear radiation is the electromagnetic radiation that occurs in nuclear reactions. Nuclear radiation is usually highly penetrating so can be very hazardous, but only high-energy electromagnetic radiation is hazardous. Nuclear radiation mainly consists of gamma rays and other high-energy electromagnetic rays as well as small particles such as electrons and neutrinos. Electromagnetic radiation only consists of photons.”  X-rays are nuclear radiation, which is why your doctor or dentist lays a lead-filled shield over you (and flees the room) before taking an X-ray image, but microwaves are not nuclear radiation, which is why you can “nuke” a corndog in the nude with your arms around the unit without doing yourself any (physical) harm.
As the raw food enthusiasts refuse to let us forget any form of cooking can alter the nutritional value of food (whether with heat or without (with acid, for instance, as in ceviche, salt or alcohol in the case of gravlax, or through fermentation as in the case of cheese and yogurt). What they are less enthusiastic to have us know is that it alters the nutrition very very little — and not always negatively. Both lycopene and biotin are more available when heated. 
3) Microwave ovens were invented by NASA. No. Percy Spencer, who was working at government contractor Raytheon, on radar technology during WWII, noticed that the microwave radar bursts he was experimenting with melted the chocolate bar he had in his pocket. After running some other food projects (resulting in the world’s first microwaved popcorn and an egg exploding in a coworker’s face) he developed a cooker he called the Radarange. The first model was 6 feet tall. A countertop model wasn’t available until 1967.
4) Microwave ovens cook food from the inside out. No. Microwave ovens cook through molecular agitation. “When exposed to microwave energy the water molecules in the food try to aline[sic] themselves with the rapidly time-varying electromagnetic field. [. . .] The oscillating molecules rub against each other and heat is generated by this intermolecular friction. Heat transfer by convection and/or conduction is a secondary process which occurs after the outer surface of the food has been exposed to the microwave excitation.”  Uneven heating, such as almost always occurs when cooking butter in a microwave oven, or heating primarily on edges or center of food is caused by the distribution of water molecules. If you are heating a piece of chicken which has dried out on the edges, even imperceptibly, then the moister center will become hotter because it has more water molecules to excite.
5) Microwave ovens are an inefficient cooking method. Not even! While not suited to all kinds of cooking (one cannot use a microwave for canning, or to slow-cook a roast, for instance) microwave ovens not only use dramatically less energy to cook than gas or electric ranges, but they use this small amount of energy for a remarkably short time, too. Just look at this impressive chart:6) Microwaving plastic allows it to leach badness into your food. Sadly, this is sometimes true. Keep in mind what the FDA says: “As is the case when foods are in direct contact with any packaging material, small, measurable amounts of the packaging materials may migrate into food and can be consumed with it.” I imagine that when you heat the food and its container that the possibility for interchange, while the molecules are, essentially, freaking out, is greater. It has long been recommended that glass and ceramic vessels, which are essentially inert and also not very porous or permeable, be the standard for cooking in microwave ovens. But this issue flared into prominence during the Bisphenol A (BPA) scare. BPA has been used since the 60s — and not just in plastics — so keep that in mind. There may be other ingredients and coatings we haven’t determined toxicity of yet. If you are a frequent microwave oven user don’t use plastic! If you aren’t a frequent user then use your best judgement. I don’t use the microwave terribly often and when I do I avoid plastic only if convenient. (If I can cover a bowl with an overturned plate I will but if I’m steaming something under plastic wrap or heating a commercial frozen dinner I shrug and hope for the best.) This may be outside your comfort zone. Me, I’m hard on the research and lax on the action.
Also worth noting: “The term “microwave safe” is not regulated by the government, so it has no verifiable meaning.”  Also, since the whole BPA thing happened relatively recently (just a few years ago) and the FDA is as slow-moving and ponderous as a Vogon** institution “microwave safe” may not necessarily reflect an absence of BPA on all labels yet.
There you have it: microwave ovens are quite safe, provided one does not use plastic or metal in them, and they are incredibly efficient. I knew the co-op folks wouldn’t steer me wrong!
* The University of Bonn, Germany scientifically proved that even a half-load of dishes washed in the machine uses less soap, water, and electricity. At least, that was their stand in 2005. In their 2011 revisitation of this study they changed their stance somewhat: machines are still the winner if washing a full load but for partial loads hand-washing ties and sometimes outperforms if carefully laid-out “Best Practices” are utilized. This is seriously one of my favorite non-Ignoble Prize scientific studies of all time. 80 bilingual pages, carefully detailed, with dozens of cited sources and 14 charts — all devoted to the best way to wash dishes.
** Vogons, for those of you poor souls who haven’t gloried in Douglas Adams’ Hitchhiker’s Guide to the Galaxy series, are hideous civil servants who are “one of the most unpleasant races in the Galaxy — not actually evil, but bad-tempered, bureaucratic, officious and callous. they wouldn’t even lift a finger to save their own grandmothers from the Ravenous Bugblatter Beast of Traal without orders signed in triplicate, sent in, sent back, queried, lost, found, subjected to public inquiry, lost again, and finally buried in soft peat for three months and recycled as firelighters.”
 “Use Your Microwave Safely” (http://www.fda.gov/ForConsumers/ConsumerUpdates/ucm048953.htm) Accessed 02/18/15.
 “Difference Between Electromagnetic Radiation and Nuclear Radiation” (http://www.differencebetween.com/difference-between-electromagnetic-radiation-and-vs-nuclear-radiation/) Posted 12/23/11. Accessed 03/04/15.
 Katz, David. “The Raw Food Diet, Overcooked.” (http://www.huffingtonpost.com/david-katz-md/raw-food-diet_b_2015598.html) Posted 10/25/2012. Accessed 03/04/15.
 Wikipedia: “Percy Spencer” (http://en.wikipedia.org/wiki/Percy_Spencer) Accessed 03/04/15.
 Hagberg, Calvin and Graff, David. “SP-202 Aerospace Food Technology: Airborne Microwave Oven Development.” (http://history.nasa.gov/SP-202/sess6.3.htm) Accessed 03/04/15.
 Meier, Alan and Mitchell-Jackson, Jennifer. “Cooking with Less Gas” (http://www.homeenergy.org/show/article/id/244) Posted 05/01/01. Accessed 03/04/15.
 “Bisphenol A (BPA): Use in Food Contact Application” (http://www.fda.gov/NewsEvents/PublicHealthFocus/ucm064437.htm) Posted 01/10, updated 11/14. Accessed 02/18/15.
 Howard, Brian Clark. “11 Surprising Facts and Myths About Microwave Ovens” (http://www.goodhousekeeping.com/recipes/microwave-radiation-ovens-460709) Accessed 02/18/15.