Fossils belonging to the genus Homo, dating as far back as two million years ago, exhibit uniquely efficient features suggesting that early humans had evolved to become exceptional endurance runners. Although they did not have the cushion or stability-control features provided in our modern day running shoes, our early human ancestors experienced far less of the running-related injuries we experience today. The injury rate has been estimated as high as 90% annually for Americans training for a marathon and as high as 79% annually for all American endurance runners. There is an injury epidemic in conventionally shod populations that does not exist in the habitually unshod or minimally shod populations around the world. This has led many to conclude that the recent advent of highly technological shoes might be the problem. Although current literature has been inconclusive, there are two main limitations in virtually all of the studies: 1) transition phases of less than three months and 2) transition phases without rehabilitation exercises. These two aspects are key to the treatment of the structural consequences on the muscles and tendons of the foot and calf that habitually shod individuals have faced. This study includes a discussion of the cumulative consequences that lifelong shoe usage has on the development of the feet and lower legs. I propose a 78-week study that addresses the limitations of past studies by implementing a gradual, 32-week, multi-shoe transition complemented by an evidence-based rehabilitation program. I believe that this approach will restore strength and elasticity to muscles and tendons that have been inhibited by lifelong usage of overconstructed shoes and adequately prepare runners for the increased demand brought on by a­­­­­ changing running mechanic. This comprehensive, multifaceted transition plan to a fully minimalist shoe will provide novel insight into the ongoing barefoot debate. Can this approach finally demonstrate the proposed benefits of losing the shoes?