After considering Dr. Thomas' general points above, you really need to dig deep into each program's description and contact the current interns/residents (depending on what positions you're applying to). There are amazing training programs in both academia and private practice. Unfortunately, there are also some sub-par ones. In addition, you want to find a program that is a great fit for you and vice-versa. Applying someplace just because of reputation is not always a great idea. For example, if well known and reputable rotating internship program lists 65% time spent in ER throughout the year; you don't like ER/critical care medicine and want to pursue an internal medicine residency. One can conclude that this program would not be a great fit for you and programs that have less ER time and allow for additional time on other specialty services would be more appropriate.