There's a popular conception that microwave ovens zap all the good stuff in our foods, like essential vitamins and minerals. But is it true?
The answer is no. And in fact, microwave ovens often retain more nutrients in our food than conventional cooking.
All cooking degrades the amount of nutrients in our food, but there are several factors to consider, including the amount of heat being applied, the amount of water used, cooking time, and the nutrients involved (e.g. folic acid and vitamins B and C, which are found in vegetables, are the most heat-sensitive water soluble vitamins).
Microwaves, because they tend to involve shorter cooking times and less heat, tend to exert less destructive effects. Unless you nuke the absolute hell out of your foods, particularly those rich in vitamin B12. Heat forces this vitamin to convert into an inactive form. So if you microwave your foods above the boiling point, you're facilitating the process beyond conventional cooking. But this effect tends to get offset by shorter cooking times. And because less water tends to be used when microwaving vegetables, nutrients don't leach out as much.
Ultimately, as this study suggests, "there are only slight differences between microwave and conventional cooking on vitamin retention in foods." Your best bet, however, is to steam your vegetables.
Now, there are a couple of caveats here. A 2003 study showed that microwaving broccoli causes it to lose 74% or more of its phenolic compounds, while boiling causes it to lose 66%. And don't nuke human milk; it decreases the potency of anti-infective agents.