The Caliciviridae comprise a new family of single-stranded RNA viruses. While human caliciviruses cause gastroenteritis, the animal caliciviruses cause a wide range of diseases. We have determined the three-dimensional structure of a primate calicivirus using electron cryomicroscopy and computer image-processing techniques. Calicivirus is one of the rare animal viruses whose capsid is made of a single structural protein. The three-dimensional structure of the virus is distinct from that of any other animal virus. However, there are several architectural similarities with plant viruses such as tomato bushy stunt virus and turnip crinkle virus. The calicivirions are 405 A in diameter and exhibit T = 3 icosahedral symmetry. The main features of the three-dimensional structure are the 32 large surface hollows, 50 A deep and 90 A wide, at the icosahedral 5-fold and 3-fold axes, and the 90 distinctive arch-like capsomeres surrounding these hollows at the local and strict 2-fold axes. Each capsomere is a dimer of the capsid protein. Despite noticeable differences, the three quasi-equivalent subunits show common structural features: the upper bilobed domain, the central stem domain, and the lower shell domain. The 2-fold related capsid proteins interact through the bilobed domains to form the top of the arch. The structural differences between the connectors of the stem and the shell domain among the three subunits suggest the presence of a hinge region that may facilitate the capsid protein to adapt to the three quasi-equivalent environments of the T = 3 icosahedral structure. The shell domains of the pentavalent and hexavalent capsid proteins associate to form a continuous shell between the radii of 115 and 150 A. A beta-barrel structure has been suggested for the shell domain. The mass density in the inner shell between the radius of 85 and 110 A may contain a portion of the capsid protein interacting with the RNA. The features between the 45 and 85 A radius are suggestive of ordered RNA.