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We investigated the effects of whey protein (WP) supplementation on body composition and physical performance in soldiers participating in Army Initial Entry Training (IET). Sixty-nine, male United States Army soldiers volunteered for supplementation with either twice daily whey protein (WP, 77 g/day protein, ~580 kcal/day; n = 34, age = 19 ± 1 year, height = 173 ± 6 cm, weight = 73.4 ± 12.7 kg) or energy-matched carbohydrate (CHO) drinks (CHO, 127 g/day carbohydrate, ~580 kcal/day; n = 35, age = 19 ± 1 year, height = 173 ± 5 cm, weight = 72.3 ± 10.9 kg) for eight weeks during IET. Physical performance was evaluated using the Army Physical Fitness Test during weeks two and eight. Body composition was assessed using 7-site skinfold assessment during weeks one and nine. Post-testing push-up performance averaged 7 repetitions higher in the WP compared to the CHO group (F = 10.1, p < 0.001) when controlling for baseline. There was a significant decrease in fat mass at post-training (F = 4.63, p = 0.04), but no significant change in run performance (F = 3.50, p = 0.065) or fat-free mass (F = 0.70, p = 0.41). Effect sizes for fat-free mass gains were large for both the WP (Cohen’s d = 0.44) and CHO (Cohen’s d = 0.42) groups. WP had a large effect on fat mass (FM) loss (Cohen’s d = −0.67), while CHO had a medium effect (Cohen’s d = −0.40). Twice daily supplementation with WP improved push-up performance and potentiated reductions in fat mass during IET training in comparison to CHO supplementation.

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