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Microbial organization in biofilms plays an important role in health and disease. This microbial lifestyle can protect its host against pathogens and contribute to the metabolism of nutrients. On the other hand, pathogenic biofilms can increase the morbidity and mortality of patients, raising the economic cost of infections. Here, we describe how biofilm is organized, its role in different scenarios in the human body and discuss how metagenomic studies has contributed to understand the microbial diversity that interact with the host. It is currently known that many biofilms in the human body may have a polymicrobial composition. In the context of infectious diseases, this composition may limit therapeutic approaches to combat biofilms even more. Thus, describing microbial diversity could help to guide therapeutic decisions.