Abstract The gastrointestinal and urogenital tracts are complex microbial habitats, which for the most part, are infection-free throughout life. Given the diversity of the world’s people, the enormous variation in diet and differences in climate, sexual practices, and exposure to antimicrobials which disrupt and change the flora, it is quite remarkable that naturally occurring infections are not even more common than reported. The composition, dynamics and structure of the normal flora biofilms appear to play a role in protecting the host from infectious upset. Specifically, lactobacilli and in the gut bifidobacteria, have been found to possess properties which enhance the host’s ability to compete against pathogens. The search for ‘good’ probiotic organisms continues, but recent findings of biosurfactant production and an ability to colonize the vagina, suggest that such strains do exist. Molecular typing has made it possible to follow the strains as they colonize or move through the host, and to investigate the genetic basis for their capabilities. Increasing concerns over drug resistance, and a growing desire by patients to have a more natural approach to their health management, is driving further scientific and clinical enquiry. This has led to some studies showing that potentially nutrients can be used to regulate, restore and stimulate the normal flora. Also of interest is the ability of probiotic organisms to reduce the risk of device-associated infections, and to deliver vaccines to the mucosal tissue. Subject to availability of grant funding for this non-traditional approach, the next 10 years should see some major breakthroughs of great benefit to the health of people around the globe.