The vast majority of cells in humans are of microbial origin. Microbial species harbored by humans include commensal as well as pathogenic organisms and are present either as planktonic cells or incorporated into biofilms. Pathogenic microbes, as components of biofilms can result in infections, and at times can initiate systemic diseases. The extracellular matrix encapsulating biofilms prevent conventional antimicrobials from functioning effectively. New approaches to characterize biofilms are being developed due to recent advancements in science and technology. These methods are proving to be key in studying the control and containment of pathogens. Characterization of biofilm structure and function coupled with a systems approach that includes conventional microbiology in concert with molecular analytical methodologies is being used to identify novel therapeutic interventions. This methods collection describes innovative techniques that are being used to identify and characterize emerging biological and chemical methods to control biofilms and eradicate pathogens.