Living-tissue biofilms remained unrecognized until very recently, mainly as a result of traditional microbial sampling techniques or histologic processing, which disrupt the spatial organization of the tissue microorganisms. Thus, the biofilm nature of certain mucosal infections was frequently unintentionally missed or disregarded. To a large extent, the study of human tissue biofilms is still in its infancy. However, with the advent of newer methodologies, such as fluorescent in situ hybridization and endoscopic confocal laser scanning microscopy, which combine the identification of microbes with in situ, direct visualization of their relationships with each other and with their substratum, mucosal tissue biofilms are becoming easier to study and, thus, their role in human infections is becoming more apparent. This review summarizes the challenges in the study of tissue biofilms, proposes two inflammation-centered - albeit opposite - pathogenetic models of mucosal tissue biofilm infections and suggests directions for future research and novel therapeutic approaches.