AimsTo investigate differential muscle atrophy during bed-rest, the impact of a high-intensity concentric-eccentric (flywheel) resistance exercise countermeasure and muscle recovery after bed-rest.MethodsTwenty-five healthy male subjects underwent 90 dayshead-down tilt bed-rest. Volume of individual lower-limb muscles was measured via MRI before, twice during and four times up to 1 year after bed-rest. Subjects were either inactive (n=16) or performed flywheel exercise every third day of bed-rest (n=9). Functional performance was assessed via countermovement jump.ResultsOn ‘intent-to-treat’ analysis, flywheel prevented atrophy in the vasti (p<0.001) and reduced atrophy in the hip adductor/extensor adductor magnus (p=0.001) and ankle dorsiflexors/toe flexors (soleus (p<0.001), gastrocnemius medialis (p<0.001), gastrocnemius lateralis (p=0.02), and tibialis posterior with flexor digitorum longus (p=0.04)). Flywheel exercise was not effective for the hamstrings, gracilis, sartorius, peroneals and anterior tibial muscles. Muscle atrophy in vasti, soleus, gastrocnemius medialis, gastrocnemius lateralis and adductor magnus correlated with losses in countermovement jump performance. Muscle volume recovered within 90 days after bed-rest, however long-term after bed-rest, the inactive subjects only showed significantly increased muscle volume versus prebed-rest in a number of muscles including soleus (+4.3%), gastrocnemius medialis (+3.9%) and semimembranosus (+4.3%). This was not associated with greater countermovement jump performance.ConclusionThe exercise countermeasure was effective in preventing or reducing atrophy in the vasti, adductor magnus and ankle dorsiflexors/toe flexors but not the hamstrings, medial thigh muscles or peroneals and dorsiflexor muscles.Trial registration numberNCT00311571; results.