Purified Sindbis virus nucleocapsids were reacted with a variety of bifunctional protein-specific cross-linking agents. The products were analyzed in concentration-gradient polyacrylamide gels and amounts of various products determined. These studies indicated that available lysine residues within adjacent capsid proteins in purified intact nucleocapsids are separated by 6 A. The capsid proteins in intact nucleocapsids are cross-linked in a pattern predicted for discrete monomeric entities, rather than in dimeric or trimeric aggregates. Purified, soluble capsid protein exists in a conformation that differs from the arrangement of protein within nucleocapsids. These conformational differences suggest that topological changes may occur in the capsid protein during virus maturation. Cross-linked nucleocapsids that were treated with RNases resulted in the generation of RNA-free protein shells that retained hexagonal morphology, indicating that, together, the RNA and protein form the outer surface of the nucleocapsid. These data are used to produce a model of the Sindbis virus nucleocapsid in which the proteins are arranged quasi-equivalently in a T = 4 icosahedral shell.