The effect of neonatal deafferentation of the rat superior cervical ganglion (SCG) on the expression of two synaptic vesicle proteins was studied to assess the role of transsynaptic influences in the regulation of these neural antigens in the SCG. The two proteins studied were a 65 kilodalton integral membrane protein of synaptic vesicles (SV), and synapsin-1 (S-1), a synaptic vesicle phosphoprotein. Antigen levels were quantified by radioimmunoassay using antibodies directed against the proteins. Distribution of SV in control, deafferented and reinnervated ganglia from 30-day-old rats was visualized by immunohistochemical labeling. Levels of both antigens were reduced following deafferentation of the SCG on postnatal days 1-3. The reduction in S-1 levels at 30 days was less than that observed for SV. The amount of S-1 remaining in deafferented ganglia was consistent with estimates of the postsynaptic pool in the SCG reported previously. SV levels, in contrast, were reduced to 24% of control levels, suggesting that SV synthesis in principal ganglionic neurons might be affected. The time course of postnatal development of S-1 in the SCG differed from previous studies of SV expression, with significant increases occurring after the second week after birth. The differences in response to deafferentation may reflect functional differences of the two vesicle-associated proteins. These studies demonstrate that transsynaptic regulation of antigens other than those directly associated with neurotransmitters occurs in the SCG.