The interaction of the synaptic vesicle protein, synaptotagmin, and the presynaptic alpha-latrotoxin receptor, a neurexin, has been proposed to be involved in docking of synaptic vesicles at active sites or modulation of neurotransmitter release. Here I report the investigation of the domain of synaptotagmin responsible for this interaction. Pieces of synaptotagmin containing the carboxyl terminus are capable of purifying neurexins from solubilized brain homogenates. Pieces as small as a synthesized peptide corresponding to the COOH-terminal 34 amino acids are capable of enriching neurexins 100-fold. The binding of neurexins to synaptotagmin is calcium-independent and of moderate affinity. This COOH-terminal segment of synaptotagmin is conserved in all species characterized to date. Reflective of this, a synthetic peptide corresponding to the carboxyl terminus of Drosophila synaptotagmin is capable of purification of rat neurexins, suggesting the possibility that this interaction may also exist in Drosophila. I propose that the carboxyl terminus of synaptotagmin binds to the carboxyl terminus of the neurexins and that this interaction may mediate docking of synaptic vesicles or modulation of neurotransmitter release.