Isolates of mutans streptococci were obtained from the dental plaque of ten subjects before and after the subjects had been free of detectable mutans streptococci for a mean period of 14.6 weeks (range, from two to 36 weeks). The mutans streptococci had been rendered undetectable by chlorhexidine varnish treatment. Examination of the restriction endonuclease analysis (REA) patterns of the isolates revealed that all ten subjects had one strain (REA type) after re-appearance of the mutans streptococci that was identical to one that had been present before the varnish treatment. In six of the ten subjects, only one strain was detected both before and after treatment. Each of the other four subjects appeared to gain a new strain after treatment; one of the four appeared to lose one strain, and another, four strains. The ability of strains to persist after the period of undetectability seemed unrelated to their resistance to chlorhexidine or to their ability to exhibit insoluble glucan-mediated adhesion. In the subjects harboring multiple REA types, one-seventh of the tooth surfaces sampled harbored two strains simultaneously, suggesting an inability of either strain to exclude the other aggressively. Overall, the study indicated that every subject receiving chlorhexidine varnish therapy had a primary strain of mutans streptococcus that re-emerged after treatment. In contrast, secondary strains were highly susceptible to being lost or gained.