By homology screening of a rat brain library, we have isolated cDNAs that encode a novel member of the synaptophysin/connexin channel protein superfamily. The deduced protein, named synaptoporin, displays 58% amino acid identity to synaptophysin, with highly conserved transmembrane segments, but a divergent cytoplasmic tail. Northern blot analysis and PCR amplification of RNA from different rat tissues indicate expression of synaptoporin transcripts in the CNS. Antibodies against a synthetic peptide or a fusion construct encompassing the cytoplasmic tail region of synaptoporin detect a polypeptide of 37 kd that copurifies with small synaptic vesicles. Our data suggest the existence of a family of vesicular channel proteins whose members may be differently distributed among synaptic vesicle subpopulations.