Most schools with MD/PhD programs allow it. The more sizeable the MD/PhD program is, the more often it occurs. For more detailed information, I suggest you talk to the directors at each program. At some schools, like WashU, there are so many slots for MD/PhD and so few M1 applicants, that the acceptance rate from M1 is about 75%. At Penn, there's alot of M1 applicants, and I think we took 3 out of 5 applicants this year. The thing is that it's historically hard to predict because if you get a rough year you could be competing for a couple spots with 10 people. Or, if you get an easy year, you could be the only one asking for one available spot at a given school.
You can also apply MD/PhD out of second year, though then you're missing out on tuition for two years. Some schools prefer it this way, as then less comes out of their pockets.
If you're really considering doing this, I would definately suggest applying to the MSTP schools (all the top ranked schools unfortunately) and choose a program based partially on this opportunity. If you're already in med school, the combined degree offices are always happy to talk to you about these things.
Good luck!