In this study of adult and neonatal rats, we used cross-correlation analysis to detect synchronous neuronal events in hypoglossal and phrenic nerves to infer synaptic connections. We found evidence for the common excitation of medial and lateral hypoglossal motoneurones in 12 anaesthetized adult rats but not in 6 in vitro brainstem-spinal cord preparations. We did not find evidence for the common activation of phrenic and hypoglossal motoneurones in 23 adult and 10 neonatal rat preparations. We confirmed this negative result by demonstrating that 26 medullary inspiratory neurones activating phrenic motoneurones did not activate hypoglossal motoneurones in 23 adult decerebrate rats (except in one case). We also found that 15 Bötzinger expiratory neurones inhibiting phrenic motoneurones did not inhibit hypoglossal motoneurones. We conclude that: (1) motoneurones of the medial and lateral hypoglossal nerve branches receive inspiratory drive from a common premotor population in adult rats, but in neonatal rats adjacent nerve rootlets do not; (2) in both adult and neonatal rats phrenic premotor neurones do not monosynaptically excite hypoglossal motoneurones; (3) Bötzinger expiratory neurones that inhibit phrenic motoneurones do not inhibit hypoglossal motoneurones. We therefore suggest that the respiratory control of hypoglossal motoneurones is separate from that of phrenic motoneurones.