We have shown that auditory cortex projects to cholinergic cells in the pedunculopontine tegmental nucleus (PPT) and laterodorsal tegmental nucleus (LDT). PPT and LDT are the sources of cholinergic projections to the inferior colliculus, but it is not known if the cortical inputs contact the cholinergic cells that project to the inferior colliculus. We injected FluoroRuby into auditory cortex in pigmented guinea pigs to label cortical projections to PPT and LDT. In the same animals, we injected Fast Blue into the left or right inferior colliculus to label PPT and LDT cells that project to the inferior colliculus. We processed the brain to identify cholinergic cells with an antibody to choline acetyltransferase, which was visualized with a green fluorescent marker distinguishable from both FluoroRuby and Fast Blue. We then examined the PPT and LDT to determine whether boutons of FluoroRuby-labeled cortical axons were in close contact with cells that were double-labeled with the retrograde tracer and the immunolabel. Apparent contacts were observed ipsilateral and, less often, contralateral to the injected cortex. On both sides, the contacts were more numerous in PPT than in LDT. The results indicate that auditory cortex projects directly to brainstem cholinergic cells that innervate the ipsilateral or contralateral inferior colliculus. This suggests that cortical projections could elicit cholinergic effects on both sides of the auditory midbrain.