The integral membrane protein synaptophysin is one of the major polypeptide components of the small, electron-translucent, transmitter-containing vesicles in neurons and of similar vesicles in neuroendocrine (NE) cells. In an attempt to identify synaptophysin-related molecules, such as synaptoporin, it was noticed in polymerase chain reaction (PCR) experiments that products having the expected size could be amplified not only from neuronal and NE cells, but also from non-NE cells. Northern blot hybridization analyses demonstrated that certain non-NE cells express low amounts of synaptophysin mRNA although the encoded polypeptide could not be detected. These observations, however, did not explain the consistent amplification of cDNA fragments regardless of cell type. PCR products were therefore cloned and a novel type of cDNA was identified in rat and human. The partial human cDNA was completed by isolation of phage cDNA clones constructed from a human keratinocyte cell line (HaCaT) and by PCR. When used in hybridization experiments with genomic DNA, this clone recognized a single gene. The 2106 bp cDNA contains an open reading frame coding for a polypeptide of calculated molecular weight 28,565 and having an isoelectric point of 8.45. This polypeptide is very similar to synaptophysin in the four transmembrane domains and the connecting loop regions but lacks the characteristic cytoplasmic tail. Extensive PCR analyses and Northern blot hybridization experiments demonstrated that the synaptophysin-related gene is ubiquitously expressed in vitro and in vivo. To stress the ubiquity of expression in contrast to the restricted distribution of synaptophysin and synaptoporin, I propose to refer to the encoded polypeptide as pantophysin.