The human upper respiratory tract is inhabited by a diverse community of microbes. Many members of this community have a pathogenic potential and are responsible for high morbidity and mortality worldwide. An initial step in the disease process is for these microbes to colonize the upper respiratory tract. Despite significant advances in the field, our understanding of the biology at play during colonization and disease remains limited. Recent progress in method and tool development has facilitated our ability to investigate the mechanisms driving these components of pathogenesis, and these procedural innovations will be the focus of this collection. Special emphasis will be placed on model systems for studying host-pathogen interactions during colonization and disease including animal models, 2D and 3D in vitro models, organoids and polymer scaffolds. Recent developments in visualizing host-microbial interactions at, and multiplex immune cell profiling of, the mucosal surface of the upper respiratory tract are highly encouraged. Of interest for this collection are also techniques aimed at discovering and characterizing host and microbial factors involved in colonization and disease including, but not limited to, omics screens, protocols to study protein-protein interactions, and functional assays to study immune responses. This Methods Collection aims to propel research in this area by focusing on methodological advances on various aspects of microbial pathogenesis host-pathogen interactions in the upper respiratory tract.