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We examined the effect of high-load fly-wheel (targeting the lower-limb musculature and concurrent loading of the spine via shoulder restraints) and spinal movement countermeasures against lumbar spine muscle atrophy, disc and spinal morphology changes and trunk isokinetic torque loss during prolonged bed-rest. Twenty-four male subjects underwent 90 d head-down tilt bed-rest and performed either fly-wheel (FW) exercises every three days, spinal movement exercises in lying five times daily (SpMob), or no exercise (Ctrl). There was no significant impact of countermeasures on losses of isokinetic trunk flexion/extension (p≥0.65). Muscle volume change by day-89 of bed-rest in the psoas, iliacus, lumbar erector spinae, lumbar multifidus and quadratus lumborum, as measured via magnetic resonance imaging (MRI), was statistically similar in all three groups (p≥0.33). No significant effect on MRI-measures of lumbar intervertebral disc volume, spinal length and lordosis (p≥0.09) were seen either, but there was some impact (p≤0.048) on axial plane disc dimensions (greater reduction than in Ctrl) and disc height (greater increases than in Ctrl). MRI-data from subjects measured 13 and 90-days after bed-rest showed partial recovery of the spinal extensor musculature by day-13 after bed-rest with this process complete by day-90. Some changes in lumbar spine and disc morphology parameters were still persistent 90-days after bed-rest. The present results indicate that the countermeasures tested were not optimal to maintain integrity of the spine and trunk musculature during bed rest.