Probiotics are live microorganisms that, when administered in sufficient doses, provide health benefits on the host. The purpose of the study is to determine the safety of Bifidobacterium animalis subsp. lactis (B. lactis) strain BB-12 (BB-12)-supplemented yoghourt when consumed by generally healthy children. Secondary aims are to evaluate the influence of BB-12 on the faecal microbiome and changes in the microbial community. A phase I, double-blinded, randomised, placebo-controlled study was conducted in compliance with United States Food and Drug Administration guidelines for an Investigational New Drug (IND). Sixty participants were randomly assigned to consume four-ounces of the active yoghourt supplemented with BB-12 or placebo yoghourt daily for 10 days. The primary outcome was to assess safety and tolerability, assessed by the number of reported adverse events. Preliminary results show 181 non-serious adverse events were reported, with no differences between the groups. Three serious adverse events unrelated to the yoghourt interventions were reported. BB-12 supplemented yoghourt is safe and well-tolerated when consumed by healthy children. Faecal samples collected before, during and after the intervention period will be analysed using state-of-the-art DNA sequencing and analysis tools to assess the relationship between the microbiome and probiotics, and to provide novel information on the dynamics of the complex ecosystem in the human gut. This study will form the basis for future clinical trials investigating the potential effects of BB-12 supplemented yoghourt in a variety of disease states.