I am also considering IM and I have an interest in later pursuing a fellowship like GI or Cardiology. I have talked to some IM residents and faculty about this problem, and it seems that the general consensus is that you will leave more doors open if you do your IM residency at an academic program that has fellowship programs. This makes sense, because you will have more exposure to higher profile academic physicians in your field of interest. However, working at a community program without fellowships certainly wouldn't preclude you from getting a fellowship later on, however it would probably be more difficult. One way to get around this problem is to do your residency at a community hospital where you will rotate through the consult services at a larger academic hospital.
