The acute phase reaction is currently regarded as systemic inflammatory response and a component of innate unspecific immunological reaction. This complex response is regulated mainly by cytokines - pleiotropic mediators of metabolic and immunological reactions. Among cytokines representing various protein families and participating in inflammation one can distinguish pro-inflammatory and anti-inflammatory cytokines as well as a large interleukin-6 family occupying intermediate position. In the initiation of acute phase reaction participate various components such as Toll-like receptors recognizing foreign pathogens, inflammasomes activating interleukin-1, and protein kinases from the MAP family that finally activate transcription factor NF-kappaB involved in cytokine synthesis. Secreted cytokines are recognized by receptors of target cells and switch on expression of many genes, including those coding for acute phase proteins. Regulation of acute phase response is precise and includes not only transcription and translation but also stability of mRNA and its degradation, as well as inhibitory activity of microRNA. Disturbances in the course of acute phase reaction are responsible for auto-immunological and autoimmune diseases and various pathological states such as acute septic shock or chronic arthritis. Some acute phase proteins, and especially C-reactive protein, have important implications for clinical diagnostics and preventive medicine.