Yes, it will jeapordize your chances a little. At my program, for example, students are evaluated by a separate MD-PhD committee, and only students that are "exceptional" (their words, not mine, I have no idea what that means) are passed on to the MD committee if they're not accpeted for our program. I know many programs evaluate you for both automatically (off the top of my head, Stanford, Wash U., I think, but this would be a good thing to call each office and ask about). However, even with these schools your application may be processed and reviewed a bit later putting you at a slight disadvantage.
If you're worried about not getting in, first, ask yourself do I want to do MD-PhD or not? It's my personal opinion that the MD-only and MD-PhD route are sufficently different that you should firmly make up your mind between the two before you apply. If you need more time, take more time, whether you wait a year before applying or apply just to med schools and try to get in second cycle. We had a few students accepted this year who got in both MD-PhD and MD-only, and they realized they didn't know what they wanted to do, and it was just a mess for them and their families. Picking a school is hard enough without another decision you could have made months ago hanging over their heads.
Then, if you're still unsure, apply a bit more broadly than you otherwise would. Hopefully, if you apply to enough schools you'll get in somewhere, it may not be your dream school but everyone gets the same degree(s) in the end. It'll also increase your odds in terms of MD-only schools that'll consider you if you get rejected (make sure you apply to plenty of these).
In short, it'll hurt your MD-only chances just a little bit, but I suggest you take some more time to mull over MD-PhD vs. MD-only. If you're still unsure, call to make sure which schools apply broadly enough and you can overcome that small disadvantage.
hzjames said:
...MDapplicants do get rejected from many schools that they otherwise shouldn't have problem getting into MD only.
Focus more on getting in to a few schools and then selecting the best fit rather then on whether the "quality" of your application matches school "quality."