The aims of this study were to compare different tracer methods to assess whole body protein turnover during 6 h of prolonged endurance exercise when carbohydrate was ingested throughout the exercise period and to investigate whether addition of protein can improve protein balance. Eight endurance-trained athletes were studied on two different occasions at rest (4 h), during 6 h of exercise at 50% of maximal O2 uptake (in sequential order: 2.5 h of cycling, 1 h of running, and 2.5 h of cycling), and during subsequent recovery (4 h). Subjects ingested carbohydrate (CHO trial; 0.7 g CHO.kg(-1.)h(-1)) or carbohydrate/protein beverages (CHO + PRO trial; 0.7 g CHO.kg(-1).h(-1) and 0.25 g PRO.kg(-1).h(-1)) at 30-min intervals during the entire study. Whole body protein metabolism was determined by infusion of L-[1-13C]leucine, L-[2H5]phenylalanine, and [15N2]urea tracers with sampling of blood and expired breath. Leucine oxidation increased from rest to exercise [27 +/- 2.5 vs. 74 +/- 8.8 (CHO) and 85 +/- 9.5 vs. 200 +/- 16.3 mg protein.kg(-1).h(-1) (CHO + PRO), P < 0.05], whereas phenylalanine oxidation and urea production did not increase with exercise. Whole body protein balance during exercise with carbohydrate ingestion was negative (-74 +/- 8.8, -17 +/- 1.1, and -72 +/- 5.7 mg protein.kg(-1).h(-1)) when L-[1-13C]leucine, L-[2H5]phenylalanine, and [15N2]urea, respectively, were used as tracers. Addition of protein to the carbohydrate drinks resulted in a positive or less-negative protein balance (-32 +/- 16.3, 165 +/- 4.6, and 151 +/- 13.4 mg protein.kg(-1).h(-1)) when L-[1-13C]leucine, L-[2H5]phenylalanine, and [15N2]urea, respectively, were used as tracers. We conclude that, even during 6 h of exhaustive exercise in trained athletes using carbohydrate supplements, net protein oxidation does not increase compared with the resting state and/or postexercise recovery. Combined ingestion of protein and carbohydrate improves net protein balance at rest as well as during exercise and postexercise recovery.