Two of the main challenges that eukaryotic multicellular organisms faced during evolution were to eliminate and replace dying cells and to cope with invading microorganisms. The innate immune system evolved to handle both tasks: to scavenge cellular debris and to form the first line of defence against microbes. In this review, we focus on high mobility group box 1 (HMGB1) protein as a common signal that alerts the innate immune system to excessive or deregulated cell death and to microbial invasion. HMGB1, which is well known nuclear protein, has revealed unexpected facets as an extracellular mediator. The role of HMGB1 as an endogenous molecule that facilitates immune responses and has an important role in tissue homeostasis and disease will be highlighted here.