Elevated post-exercise amino acid availability has been demonstrated to enhance muscle protein synthesis acutely, but the long term impact of post-exercise protein supplementation on variables such as health, muscle soreness, and function are unclear. Healthy male U.S. Marine recruits from six platoons (U.S. Marine Corp Base, Paris Island, SC; n=387; 18.9±0.1 years, 74.7±1.1 kg, 13.8±0.4% body fat) were randomly assigned to three treatments within each platoon. Nutrients supplemented immediately post-exercise during the 54-day basic training were either Placebo (0 g carbohydrate, 0 g protein, 0 g fat); Control (8,0,3); or Protein supplement (8,10,3). Subjects and observers making measurements and data analysis were blinded to subject groupings. Compared to placebo and control groups, the protein supplemented group had an average of 33% fewer total medical visits, 28% fewer visits due to bacterial/viral infections, 37% fewer visits due to muscle/joint problems, and 83% fewer visits due to heat exhaustion. Recruits experiencing heat exhaustion had greater body mass, lean, fat, and water losses. Muscle soreness immediately post-exercise was reduced by protein supplementation versus placebo and control groups on both days 34 and 54. Post-exercise protein supplementation may not only enhance muscle protein deposition, but it also has significant potential to positively impact health, muscle soreness, and tissue hydration during prolonged intense exercise training, suggesting a potential therapeutic approach for the prevention of health problems in severely stressed exercising populations.