I flew from Amsterdam to Minneapolis in January, when I was 5 months pregnant. I also had my 2 year old daughter with me. We both went through the scanner, and they also did a little "mini" patdown because my daughter kept dancing while she was in the scanner and they could not get a clear view. As for the pat down on my daughter - it was incredibly inobtrusive, and they did not place their hands anywhere inappropriate. Certainly nowhere near the genitals. My daughter thought the whole think was a great lark and then attempted to "pat down" the agent (who thought this was the cutest thing he'd ever seen.) In fact when I was picking up our hand luggage, my daughter insisted that the agent come and sit with her and hold her hand while she was waiting. So, our experience there was entirely positive (although I realise that much of this depends upon the agent that you get.)
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I, rather stupidly, walked through the scanner without giving a second thought to the fact that I was pregnant and whether or not they were safe (it was a long trip with a toddler, I could barely articulate my name at that point!) Had I thought about it in advance, I would probably have chosen the full patdown, regardless of how intrusive I believe they can be. But after I got back I read a lot about the two different kinds of scanners, and also checked with Schiphol to see which one was used there. I believe it was the "backscatter" one, but honestly, my understanding is that neither of them poses an increased risk to pregnant women (or no more than the process of flying, anyway, in terms of radiation exposure.) I appreciate that some people have issues with the detailed images that are produced, but that doesn't bother me in the slightest. And I would have been OK with the patdown. My only concern was the radiation.