Unfortunately, very little research exists on what happens to food when we microwave it. Microwaves themselves have not been shown to increase cancer risks, despite concerns after the products first hit the market that standing to close to one might cause cancer. Such rumors have been sufficiently debunked and the regulation of microwave oven quality means this isn’t a cancer risk we need to worry about.
One of the areas where we simply don’t know enough is in what happens to plastic when we microwave it. Studies have indicated that some chemicals found in the plastic leach into food when we microwave food in plastic containers. There are many different types of plastic on the market so knowing exactly what chemicals and how much of them is challenging. Because we know so little, but we do know that some of the chemicals that might leach out can be nasty, my recommendation is to apply this precautionary principle:
Take your food out of the plastic container and place it on a glass or ceramic dish. Instead of covering your food with plastic wrap to keep your microwave clean or create a nice steaming environment, use a glass lid or towel (a paper or a fabric dish towel works great). While we don’t know that microwaving food in plastic causes cancer, those of us who want to do everything we can to lower our risk can take this approach. If you can’t remove your food from the plastic, don't worry. The data on the potential harms are still emerging and are far from being in the same category as known carcinogens like smoking and obesity.
Even if the plastic is labeled BPA-free, it might have other chemicals worth avoiding in it, so the best bet is to try to avoid these chemicals all together.
We do have some interesting work emerging on what happens to our food when we cook it in the microwave, regardless of the cooking container. We have known for some time that cooking fruits and vegetables can change the nutrient content. Recent research has shown that how we cook those foods might also result in variations in the nutrient content. One study found that microwaving broccoli resulted in a loss of 90% of vitamin C. Losses were much lower with steaming. Broccoli is a healthy food no matter how you cook it, or if you choose to eat it raw. (It certainly beats whatever you might find in a vending machine.) If you have the option to prepare broccoli by steaming or sautéing it, you will preserve more of the key nutrients. If you do microwave your broccoli, try to use as little liquid as possible.
For other vegetables and some other important nutrients in broccoli, microwaving might preserve other nutrients more than conventional cooking methods like boiling. There is no single right way to cook all foods.
I bring vegetables to the office for lunch and don’t have the option to cook them except in the microwave. I put the veggies in a glass container with minimal, if any, liquid, cover them with a paper towel and cook them for a short amount of time.
These are the little changes that you can make to lower your cancer risk even more.