The Hippo signaling pathway regulates cell proliferation, organ size and tissue regeneration through a series of kinase cascades. MST1/2 is the mammalian orthologue of the core kinase Hippo, which is crucial for the activation of downstream signaling. Additionally, MST1/2 has been reported to play important roles in cell differentiation, morphology and cytoskeleton reorganization. Recent evidence suggests that MST1/2 is involved in the regulation of T cell adhesion, migration, homing and Treg cell maturation and functions. Interestingly, these processes are not dependent on the canonical, but a non-canonical Hippo signaling pathway. More recent studies have revealed that MST1/2 mediates the innate immune response against pathogens or viruses, especially on macrophage phagocytosis as well as cytokines and ROS production. MST1/2 is associated with various diseases, such as bacterial or viral infection, inflammation-related cancer, and atherosclerosis. In this review, we summarize recent findings on the functions of MST1/2 in the innate immune response and inflammation-related diseases.