Respiratory motor output in bilateral cranial nerves is synchronized, but the underlying synchronizing mechanisms are not clear. We used an in vitro slice preparation from newborn mice to investigate the effect of systematic transsections on respiratory activity in bilateral XII nerves. Complete transsection at the midline resulted in desynchronized rhythm with reduced XII burst amplitude and duration. Transsections in the ventral or dorsal 1/3 of the midline did not desynchronize rhythm. However, transsections in the ventral 2/3 of the midline desynchronized rhythm with characteristic amplitude correlations, where large-amplitude XII-bursts on one side was synchronized with small-amplitude XII-burst on the contralateral side. These characteristic amplitude correlations suggest that hypoglossal motoneurons receive respiratory drive from bilateral sources. Retrograde labeling confirmed that commissural fibers from the pre-Bötzinger complex cross in the mid-1/3 of the midline, and that dendrites of hypoglossal motoneurons project into the contralateral XII nucleus. In conclusion, commissural fibers crossing in the mid-1/3 of the midline are required for synchronization of respiratory activity in bilateral XII nerves. Hypoglossal motoneurons receive respiratory drive from both sides of the medulla, possibly mediated by contralaterally projecting dendrites.