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Human-exoskeleton misalignment could lead to permanent damages upon the targeted limb with long-term use in rehabilitation. Hence, achieving proper alignment is necessary to ensure patient safety and an effective rehabilitative journey. In this study, a joint-based and task-based exoskeleton for upper limb rehabilitation were modeled and assessed. The assessment examined and quantified the misalignment present at the elbow joint as well as its effects on the main flexor and extensor muscles’ tendon length during elbow flexion-extension. The effects of the misalignments found for both exoskeletons resulted to be minimal in most muscles observed, except the anconeus and brachialis. The anconeus muscle demonstrated a relatively higher variation in tendon length with the joint-based exoskeleton misalignment, indicating that the task-based exoskeleton is favored for tasks that involve this particular muscle. Moreover, the brachialis demonstrated a significantly higher variation with the task-based exoskeleton misalignment, indicating that the joint-based exoskeleton is favored for tasks that involve the muscle.