A prospective study was conducted to better characterize the epidemiology of plasmid-bearing strains of Salmonella typhi in an endemic area of Lima, Peru, and to determine if plasmids were associated with specific manifestations of typhoid fever. Of 228 S. typhi isolated from patients at Cayetano Heredia University Hospital in Lima during 1987-1988, 76 (33%) contained plasmids. Ten different plasmid profiles were identified, with ten distinct plasmids present within these profiles. There was significant temporal clustering of isolates having common plasmid profiles. Two plasmids (both from the same isolate) carried antibiotic resistance genes. Two cryptic plasmids with approximate sizes of 55 and 65 kilobases (kb) appeared to be closely related, based on restriction endonuclease digestions and Southern blot analysis. An ampicillin resistance plasmid from a 1989 patient isolate differed by only a single restriction fragment from the cryptic 65-kb plasmid. No association was found between any plasmid or plasmid profile and severity or clinical manifestations of disease.