Genetic heterogeneity among closely related isolates of foot-and-mouth disease virus (FMDV) has been measured by direct sequencing of the VP1-coding-region RNA for three new FMDVs of serotype C1 and by additional sequences of RNA from previously reported isolates, all belonging to a single episode of disease [Sobrino et al., Gene 50 (1986) 149-159]. In the ten viruses compared, eight different VP1 are represented. The changes include amino acid substitutions at a critical antigenic determinant of VP1. We document that variations present in such natural isolates result in changes of the immunogenic properties of the viruses. Vaccines prepared with two of the FMDV C1 analyzed induce complete protection against an homologous virus but only partial protection against an heterologous virus in swine, the host from which these viruses were isolated.