The up-regulation of immune checkpoint molecules, such as PD-1 and CTLA4 on immune cells occur during acute infections, such as malaria, as well as during chronic persistent viral infections, including HIV and hepatitis B virus (HBV). These pathways are important for preventing immune-driven pathology, but can also limit immune-mediated clearance of the infection. The recent success of immune checkpoint blockade in cancer therapy suggests that targeting these pathways could also be effective for preventing and treating a range of infectious diseases. Here, we review our current understanding of immune checkpoint pathways in the pathogenesis of infectious diseases and discuss the potential for therapeutically targeting these pathways in this setting.