We examined the effects of a 16-day spaceflight mission on the size of muscle fibers in the rectus abdominis, external oblique and transversus abdominis muscles of adult male Fisher rats. The rats were individually housed in orbit, in contrast to the one previous spaceflight investigation of the same muscles, where the rats were group-housed pregnant females. The cross-sectional area of the muscle fibers was used as a measure of muscle atrophy or hypertrophy. The transversus, which is presumed to be the primary expiratory muscle and consequently works against internal hydrostatic pressures that are not likely to change much between 1 G and weightlessness, did not change in size. However, both the rectus abdominis (a spinal flexor) and the external oblique (a rotator of the torso), which resist gravity in the 1 G environment, showed significant signs of atrophy after extended exposure to microgravity. The atrophy of the external oblique was diametrically opposite to hypertrophy of the same muscle observed in group-housed rodents previously exposed to spaceflight. Although the two missions differed in several factors, such as the gender of the rats and mission duration, we believe that housing of the animals was the key factor that accounted for the different responses of the external oblique. Previous research has shown that group-housed rats in spaceflight exhibited seven times more rotations of their torsos than matched ground controls. Thus unloading of the musculoskeletal system may not be achieved in weightlessness when animals have the freedom to interact with each other.