Regulated proteolysis of cellular factors is pivotal to tissue development and homeostasis, whereas uncontrolled proteolytic activity is linked to disease. Type II transmembrane serine proteases (TTSPs) are expressed at the cell surface and are thus ideally located to regulate cell-cell and cell-matrix interactions. Increasing evidence demonstrates that aberrant expression of TTSPs is a hallmark of several cancers and recent studies have defined molecular mechanisms underlying TTSP-promoted carcinogenesis. In addition, new findings suggest that influenza and other respiratory viruses could exploit TTSPs to promote their spread, making these proteases potential targets for intervention in cancer and viral infections. Here, we review the role of TTSPs in tumorigenesis and viral infection and discuss potential approaches to therapy.