I don't think it matters much at all. What matters most is the quality of the institution that you train at. For example, UCSF has both a primary care and categorical track. It turns out that a large percentage of the residents in the primary care track end up pursuing fellowships. Do you think it hurts the residents? Absolutely not since UCSF is arguably the best program in the country to train at. The only potential disadvantage to consider is that you may spend a greater proportion of your residency training in the ambulatory setting and therefore devote less of your time to electives in the medicine subspecialties which may decrease your exposure/opportunities to make connections and to make an educated decision about your future career choice. You may also have less time to pursue research as well, but this certainly depends on the intricacies of the specific program. Hope this helps.
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