It is becoming increasingly accepted by consumers that live lactic acid bacteria do exert health benefits when eaten. In addition, it is also becoming recognised that not all probiotic bacteria are equal. It is now no longer just a question of providing sufficient numbers of viable bacteria in a product; industry must also provide proof of efficacy for each strain. In the early 1990s, Fonterra embarked on a programme to develop proprietary probiotic strains, and as a result, commercialised two strains, Bifidobacterium lactis HN019 and Lactobacillus rhamnosus HN001. Over the past decade, Fonterra has developed a significant body of peerreviewed published reports around these strains, including studies showing safety in animal and human trials, protection against pathogens such as Salmonella typhimurium and Escherichia coli O157:H7, modulation of human and animal immune markers at realistic dose rates, and efficacy in human clinical trials. Based on this work, HN019 and HN001 have been applied to several functional foods both by Fonterra (under the DR10 and DR20 brands, respectively) and by third parties (e.g. under the HOWARU brand by Danisco). While the 'gold standard' of proof of efficacy is a phase III clinical trial, ethical considerations as well as expense preclude the use of clinical trials as screening tools for probiotics. Therefore, biomarkers have to be employed to identify strains with probiotic utility, and to define the different positive health benefits of existing probiotic strains. However, as the mechanisms by which most probiotic bacteria exert their health benefits remain unclear, the question of which biomarkers accurately reflect efficacy in vivo remains unresolved. With recent technological advances, and the shift toward probiotics targeted to specific conditions, researchers are beginning to tease out how probiotic bacteria work, and it is this knowledge that will inform biomarker development and improve the ability to offer the market safe and effective probiotic functional foods.