Do we have to wait a few seconds to let the microwaves go away, or can we eat it immediately?
Of course, I assume that the food is not too hot to be eaten.
Yes it is completely safe. Microwaves do not linger in food. The microwaves stop as soon as your microwave stops.
A microwave is just an electromagnetic wave similar to a radio wave, but at a higher frequency. It works by exciting molecules, particularly water, in the food and giving those molecules some of its energy as heat.
Microwaves do not alter the structure or composition of molecules or atoms directly, which is what happens with ionizing radiation (gamma rays, x-rays, and UV-rays). You could cook your food with gamma rays, but you would ionize many of the particles making them radioactive.
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I'm assuming you're thinking you might have to wait for the microwaves to disappear from the food? (Edit: actually, you said so explicitly …) Well, I don't think the physical properties of microwaves work that way. ;) Interestingly, here's an article titled “Microwaved Food Isn't Safe to Eat”, which I'm personally taking with a large grain of salt; but note that of all the claimed dangers with microwaved food, the possibility of “ingesting” microwaves isn't one of them! (The article does claim health problems have arisen from the microwave field next to a microwave oven; which is contradicted by the information found on Wikipedia.)
Regarding the microwaves going away: Microwaves are essentially the same kind of electromagnetic radiation as light, just in a different frequency range. If the oven's light-bulb gets turned off at the same time as the magnetron, the microwaves should be gone by the time you stop seeing the light.
Regarding safety: I have eaten microwaved food on several occasions with no ill consequence. Of course, there may be long term effects I'm not aware of but you might try asking about that on a biology-oriented site since hobodave has already ruled out radioactivity from the physics perspective.
I am not a biologist, micro- or otherwise. I'm also not a nutritionist, but I've heard that microwaves can reduce the nutritional value of food. I'm certainly willing to believe that the interactions are small and complicated enough to be very difficult to fully observe. Further, I can believe that the pro-microwave and anti-microwave lobbies are pretty lop-sided in terms of funding and effort. Finally, it seems to me that nutrition is a complex enough subject for a lot of nutritional advice to be under constant revision.
Given those thoughts, I see the following possible approaches: