Is it dangerous to cook in a microwave?
No. The only thing microwaves do to food molecules is make them move—a lot, which creates the heat that warms up food. A microwave uses radio waves (larger waves than, say, light waves) at a frequency where they are absorbed by water, fats, and sugars, but not by plastics, glass, or ceramics. When the radio waves are absorbed, they are converted directly into atomic motion, or heat.
Evidence: Every so often a nonpeer-reviewed study comes out claiming a "microwave effect," but in scientific literature there are many more studies that contend microwaves are perfectly safe.
Keep in mind: Cooking with microwaves is tricky. Heat is nonuniform, which means certain places can get heated much more than others. This can produce undesirable changes to the look and feel of the food, but does not affect its molecular structure.
—Ashim K. Datta, Ph.D., professor of biological and environmental engineering at Cornell University