Bacteriocins, specific and highly potent protein antibiotics, have been long been expected to enter the working pharmacopeia. Despite laboratory experiments demonstrating their effectiveness against a wide range of gastrointestinal pathogens, attempts to reproduce such killing activity by using live bacteriocin-producing bacteria in animal gastrointestinal systems repeatedly failed. This raised doubts about the potential of the bacteriocins as in vivo antibiotics. Thus, though some bacteriocins have been employed in food preservation and processing, none have been applied directly as medicine. Recent experiments, based on an improved theoretical understanding of microbial ecology, demonstrate the in vivo activity of bacteriocins, the potential importance of bacteriocins as antibiotics, and the role that bacteriocins play in antibiotic resistance. Meanwhile, several kinds of bacteriocins have been proposed for applications in gastrointestinal microbiology, as well as for the use of probiotics to reduce dental caries and improve oral hygiene. Unfortunately, much of the probiotic-oriented research appears to be pursued without reference to resistance and the role of the bacteriocins in a community of bacteria. This leads to continued confusion regarding the interpretation of experimental results and mistaken assessments, positive and negative, of bacteriocins' therapeutic potential. A study of microbial ecology should be incorporated in the drug development process in order to apply bacteriocins most effectively.