It is almost a century since it was first proposed that maintaining a high population of bifidobacteria in the large intestine is associated with good intestinal health and longevity. In the ensuing time, numerous studies have substantiated this link between good intestinal health and high bifidobacteria numbers. However, there is still no really convincing data available to support a specific health claim for ingesting any particular strain of bifidobacteria. In clinical feed studies carried out to date with bifidobacteria, very little knowledge was available on the ecological suitability of probiotic strains to the intestinal conditions within a particular group of test individuals. This lack of knowledge is a significant factor hindering proper scientific analysis of the data generated, and also the rational selection of suitable probiotic strains. This review will address advances made in the methodologies for detecting, differentiating and phylogenetically characterizing bifidobacteria. These methodologies will provide the necessary tracking and characterization tools to investigate the relationship between different bifidobacteria and different intestinal ecological conditions. These studies are necessary to direct selection of bifidobacteria with the desired efficacy for probiotic uses.