Autonomic innervations of the mucosa in the middle ear and pharynx were investigated by retrograde labelling of the autonomic ganglia with horseradish peroxidase (HRP). Of the sympathetic ganglia, the superior cervical ganglion (SCG), middle cervical ganglion (MCG) and stellate ganglion (StG) were examined, and of the parasympathetic ganglia, the pterygopalatine ganglion (PpG) and the otic ganglion (OtG) were examined. Sympathetic innervation of the middle ear mucosa was accomplished by fibers originating in the ipsilateral SCG, but not by those originating in the MSG or StG. Parasympathetic innervation was by fibers originating in the ipsilateral PpG, but not by those originating in the OtG. The epipharynx received sympathetic innervation from the ipsilateral SCG, but not from the MCG or StG. Its parasympathetic innervation was from the PpG bilaterally, but not from the OtG. Sympathetic innervation of the mesopharynx was supplied by the SCG, MCG and StG, but no parasympathetic supply came from the PpG or the OtG. Sympathetic innervation was bilateral, but predominantly from the ipsilateral side. The hypopharynx resembled the mesopharynx, but had more innervation from the MCG and StG.