The innate immune system is in the vanguard of host defenses against infection. Recognition of invasive microbial pathogens is mediated by pattern recognition receptors on the surface of immune cells that recognize pathogen-associated molecular motifs. Considerable progress has been made in recent years in understanding how bacterial products initiate sepsis. In gram-negative sepsis, the LPS-binding protein (LBP), CD14 and the recently identified Toll-like receptor 4 (TLR4) are key molecules for the recognition of endotoxin (lipopolysaccharide, LPS) by cells of the myelomonocytic lineage. In gram-positive sepsis, components of the bacterial cell wall (peptidoglycan, PGN; lipoteichoic acids, LTA) have been shown to activate myeloid cells through an interaction with a receptor complex composed of CD14, TLR2 and perhaps also TLR6 (PGN) or CD14 and TLR4 (LTA). By contrast, gram-positive exotoxins act as superantigens and directly stimulate T lymphocytes by cross-linking the MHC class II of antigen presenting cells to specific chains of the T cell receptor. Immune cells activated by microbial pathogens release numerous effector molecules, which orchestrate the innate and adaptive host defenses. Furthermore, bacteria and microbial toxins directly activate the complement and coagulation systems, which play an important part in the host defensive response. Severe sepsis and septic shock can be viewed as clinical manifestations of a failing innate immune response that ultimately results in an overstimulation of the physiological host response. The pathogenesis of sepsis is far more complex that was initially anticipated. However, combined research efforts of basic scientists and clinical investigators continue to provide critical information for the identification of novel therapeutic targets. The exciting results obtained recently with treatment strategies designed to correct coagulation abnormalities occurring during sepsis are an example of how research may ultimately translate into improved patient care.