Head-down (-6 degrees) bed rest, a microgravity simulation model in humans, leads to muscular atrophy of the lower limbs. Magnetic Resonance Imaging (MRI) at 0.5 tesla was performed at 1 year intervals on the same six volunteers (except one) before and after 1 month bed rest. Three of the six subjects were daily exposed in a lying position to LBNP (lower body negative pressure), a countermeasure to cardiovascular deconditioning (LBNP group). The groups were exchanged the second year. After bed rest, the quadriceps of the thigh lost uniformly 11% of its cross section area (CSA) and the triceps of the leg 10.5%, with 12.8% lost from the deeper soleus versus 8.5% from the gastrocnemius (p < 0.05). LBNP produced no effect on these changes. The MRI signal intensity of muscles exhibited a trend toward higher values after bed rest although without statistical significance. MRI allowing for noninvasive and reliable quantification of muscle fibers of the lower limbs is an excellent procedure for the assessment of muscle disuse and countermeasures.