The surgical approach has been the predominate mode of caries management for the past 150 years. Dentistry has, however, in recent years moved toward an antibiotic/antimicrobial model of disease management. This approach, however, raises serious questions: (1) do the antibiotic/antimicrobial agents (chlorhexidine, povidone iodine, fluoride, etc) kill all offending organisms?; (2) if so, do the agents preclude the re-entry of the same organisms from external sources?; and (3) if the agents do kill all the offending organisms, do any remaining pathogenic organisms have selective advantage in repopulating the tooth surfaces? To overcome the problems inherent in an antibiotic/antimicrobial approach, probiotic methods are currently under study as means of caries management. This paper discusses probiotic approaches, such as genetically modified Streptococcus mutans and targeted antimicrobials in the management of dental caries. Implications for this approach in the management of other diseases are also presented.