You don't apply to fellowship directly out of medical school. When applying to fellowships, Step I scores matter very little. The quality of your IM program and your research/publications matter the most. Of course, you could indirectly say Step I scores are important because they will help you attain a better IM residency. But there are a lot of GI fellowships in the country. You don't have to attend a top 30 IM program if you want to get a GI fellowship. Research is more important than Step I scores. Get a decent score on Step I and then starting looking for GI research.
Something that is overlooked is your performance as a resident. Remember that your best chances of attaining a fellowship is at your own program. And your own program will place a heavy emphasis on your reputation and performance as a resident. Aspring fellows focus too much on research and not enough on their performance as a resident. I have seen many residents make this mistake. They will be so consumed with the application process and their research that they ignore their duties as a resident. Thus otherwise research qualified residents will get lukewarm or unimpressive letters and not match in any program whereas stellar residents with average research will match somewhere.
