Microwave cooking is far removed from traditional cooking practices as it literally radiates food as it heats. There simply isn’t enough research to determine the safety entirely. My general perspective is that it is always best to instinctively choose things in their most natural state. I personally do not own (and have never owned) a microwave.
No matter how its done, cooking fruits and vegies changes their structure and often destroys vital nutrients. The type of cooking preparation you choose determines how much is destroyed. When cooking in water, you literally leach out the nutrients and throw them out. Fruits and vegies contain vitamins, minerals and phytonutrients (plant nutrients). Phytonutrients have poor heating temperatures and are easily destroyed. Minerals are generally quite hardy to increased temperatures but water-soluble vitamins (vitamins c and b’s) can’t survive the process of microwaving due to heating of water (microwaves work by molecular friction – heating the water molecules inside foods). Fat-soluble vitamins may be safer but the act of heating potentially changes their structure and thus their nutritional value.
The macronutrients – fats, carbs and protein are a little different. Microwaves have been shown to change the structure of proteins. An interesting (small) study showed that amino acid structure changes from the healthy to the toxic type was produced from microwaving. The research is limited so I won’t make a blanket statement. It does make you question the safety and should certainly make you think twice before you microwave a child’s bottle!
We’re a funny bunch us humans. We take beautiful healthy food, nuke it in the microwave and then wonder why we are nutritional deficient. We eat heavily processed and tasteless food in larger quantities because we are nutritionally deficient and perpetuate the cycle of malnourished overfeeding.