Amphiphysin is a protein peripherally associated with synaptic vesicles. It is expressed in many neurons, certain endocrine cell types, and spermatocytes. Autoantibodies against amphiphysin occur in patients afflicted with a rare neurologic autoimmune disease, paraneoplastic Stiff-Man syndrome. To provide a basis for the understanding of anti-amphiphysin autoimmunity, we have cloned cDNAs and determined the primary structure of human amphiphysin. Comparison with chicken amphiphysin defines domains of low and high amino acid sequence conservation. As a candidate for heritable disorders of the nervous system, endocrine tissues or male fertility, the human amphiphysin gene was mapped to chromosome 7, region p13-p14.