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Both chronic microgravity exposure and long-duration bed rest induce cardiac atrophy, which leads to reduced standing stroke volume and orthostatic intolerance. However, despite the fact that women appear to be more susceptible to postspaceflight presyncope and orthostatic hypotension than male astronauts, most previous high-resolution studies of cardiac morphology following microgravity have been performed only in men. Because female athletes have less physiological hypertrophy than male athletes, we reasoned that they also might have altered physiological cardiac atrophy after bed rest. Magnetic resonance imaging was performed in 24 healthy young women (32.1 ± 4 yr) to measure left ventricular (LV) and right ventricular (RV) mass, volumes, and morphology accurately before and after 60 days of 6° head-down tilt (HDT) bed rest. Subjects were matched and then randomly assigned to sedentary bed rest (controls, n = 8) or two treatment groups consisting of 1) exercise training using supine treadmill running within lower body negative pressure plus resistive training ( n = 8), or 2) protein (0.45 g·kg−1·day−1increase) plus branched-chain amino acid (BCAA) (7.2 g/day) supplementation ( n = 8). After sedentary bed rest without nutritional supplementation, there were significant reductions in LV (96 ± 26 to 77 ± 25 ml; P = 0.03) and RV volumes (104 ± 33 to 86 ± 25 ml; P = 0.02), LV (2.2 ± 0.2 to 2.0 ± 0.2 g/kg; P = 0.003) and RV masses (0.8 ± 0.1 to 0.6 ± 0.1 g/kg; P < 0.001), and the length of the major axis of the LV (90 ± 6 to 84 ± 7 mm. P < 0.001), similar to what has been observed previously in men (8.0%; Perhonen MA, Franco F, Lane LD, Buckey JC, Blomqvist Zerwekh JE, Peshock RM, Weatherall PT, Levine BD. J Appl Physiol 91: 645–653, 2001). In contrast, there were no significant reductions in LV or RV volumes in the exercise-trained group, and the length of the major axis was preserved. Moreover, there were significant increases in LV (1.9 ± 0.4 to 2.3 ± 0.3 g/kg; P < 0.001) and RV masses (0.7 ± 0.1 to 0.8 ± 0.2 g/kg; P = 0.002), as well as mean wall thickness (9 ± 2 to 11 ± 1 mm; P = 0.02). The interaction between sedentary and exercise LV and RV masses was highly significant ( P < 0.0001). Protein and BCAA supplementation led to an intermediate phenotype with no change in LV or RV mass after bed rest, but there remained a significant reduction in LV volume (103 ± 14 to 80 ± 16 ml; P = 0.02) and major-axis length (91 ± 5 to 88 ± 7 mm; P = 0.003). All subjects lost an equivalent amount of body mass (3.4 ± 0.2 kg control; 3.1 ± 0.04 kg exercise; 2.8 ± 0.1 kg protein). Cardiac atrophy occurs in women similar to men following sedentary 60 days HDT bed rest. However, exercise training and, to a lesser extent, protein supplementation may be potential countermeasures to the cardiac atrophy associated with chronic unloading conditions such as in spaceflight and prolonged bed rest.