Studies using biophysical techniques suggest a highly structured organization of calcium channels at the presynaptic transmitter release face (Llinás et al., 1981; Stanley, 1993), but it has not as yet proved possible to localize identified channels at the required nanometer level of resolution. We have used atomic force microscopy on the calyx-type nerve terminal of the chick ciliary ganglion to localize single calcium channels tagged via biotinylated omega-conotoxin GVIA to avidin-coated 30 nm gold particles. Calcium channels were in low (modal value approximately < or = 1 per micron 2) and high (modal value approximately 55 per micron 2) density areas and exhibited a prominent interchannel spacing of 40 nm, indicating an intermolecular linkage. Particles were observed in clusters and short linear or parallel linear arrays, groupings that may reflect calcium channel organization at the transmitter release site.