Variation in cyclical behaviors can be partitioned among hierarchical levels. Understanding how variation is partitioned is important for identifying what level is most likely associated with differences in performance. The effect of recurrent laryngeal nerve lesion on swallowing kinematics and muscle function is highly variable among individuals. However whether variation is partitioned similarly among individuals, lesion status, and swallow cycle in kinematics and EMG variables is unknown. We hypothesize that because muscle activation patterns produce kinematics, we will see similar patterns of hierarchical variation in kinematics and EMG. We recorded high speed videofluoroscopy and EMG of six infant pigs drinking milk mixed with barium. We digitized radiopaque markers to calculate three kinematic variables for every swallow. We calculated duration and timing of onset of muscle activity during swallows for seven oropharyngeal muscles before and after recurrent laryngeal nerve lesion. We scored swallows for successful airway protection using an ordinal scale. We used a hierarchical nested model to partition variance among airway protection, cycle, lesion status, and individual. Variance partitioning did not follow similar patterns in EMG and kinematic data. Between cycle variation was greatest in kinematics, while between individual variation was greatest in timing and duration of EMGs. The amount of variation attributed to experimental factors is highly variable though consistently less than non-experimental factors. The different patterns of hierarchical variation in muscle activation and kinematics suggest potentially different responses to functional challenges.