We have used pre-embedding EM immunohistochemical methods to obtain quantitative data on the frequency and post-synaptic targets of 5-hydroxytryptamine-immunoreactive (5-HT-IR) boutons within the rat V motor nucleus. Thirteen percent (69/531) of all synaptic contacts in the motor nucleus involved 5-HT-IR boutons. Seventy-four percent of 5-HT-IR boutons made axo-dendritic contacts, 20% axo-somatic contacts, and 6% axo-axonic contacts. We conclude that a significant fraction of boutons in the motor nucleus are 5-HT-IR and most contribute to postsynaptic rather than presynaptic effects on trigeminal motoneurones.