Current research continues to improve the treatment options available to clinicians for oral bacteriotherapy. Recently, a greater understanding of the role of endogenous digestive microflora has generated renewed interest in the potential of oral bacteriotherapy for the management of a wide spectrum of gastrointestinal and systemic disorders. Several treatment strategies for oral bacteriotherapy have already entered clinical trials and it is hoped that some of these strategies will become widely available in the near future. This review summarises the current status of oral probiotic preparations for bacteriotherapy and discusses any obstacles to their successful clinical development. Newer probiotic preparations include high potency preparations that are greatly enriched in lactic acid bacteria, both in terms of bacterial concentrations and the number of bacterial strains. These preparations have a greater potential for clinical effectiveness than traditional preparations and are entering clinical evaluation especially in patients with inflammatory bowel disease and pouchitis, irritable bowel syndrome, or cryptosporidiosis. The pitfalls of previous clinical investigations of traditional probiotic preparations and the perils of future clinical trials with high potency preparations are discussed in the context of unmet needs and realistic expectations of success. Although considerable progress has been made in oral bacteriotherapy, focused efforts by basic scientists and clinical investigators and continued support from pharmaceutical companies is required to successfully develop probiotics for use in clinical medicine. Newer high potency probiotic preparations appear to have a great advantage over traditional preparations and should be the area of most active biomedical research in the field.