Serine proteases form a large family of protein-cleaving enzymes that play an essential role in processes like blood coagulation, apoptosis and inflammation. Immune cells express a wide variety of serine proteases such as granzymes in cytotoxic lymphocytes, neutrophil elastase, cathepsin G and proteinase 3 in neutrophils and chymase and tryptase in mast cells. Regulation of proteolysis induced by these serine proteases is essential to prevent self-induced damage. Hence, there are specialized serine protease inhibitors, serpins, which are broadly distributed. Here, we discuss the function of human serine proteases in inflammation, apoptosis and tissue remodeling. Furthermore, we address their impact on development and progression of immune mediated-diseases. Understanding the mode of action of serine proteases will help to unravel molecular processes involved in immunological disorders and will facilitate the identification of new therapeutic targets.