The treatment of infectious diarrhea poses multiple challenges. The causes of infectious diarrhea are diverse, ranging from bacterial to viral to fungal, and the types of available treatments are equally diverse. Traditional therapeutic approaches with antibiotics, changes in diet, and oral rehydration therapy have been useful, but the need for alternative treatments exists. The use of beneficial living organisms or biotherapeutic agents has been investigated and found safe and effective for various types of infectious diarrhea and the treatment of Clostridium difficile disease. Although there are numerous types of microbial preparations available, only a few are backed by large, placebo-controlled clinical trials. The microbial agents with adequate scientific evidence include Saccharomyces boulardii, Lactobacillus rhamnosus GG, and several species of bifidobacteria and lactobacilli. The scientific evidence for these agents is reviewed and analyzed in this article.