The innate immune system recognizes and rapidly kills invading bacteria via different mechanisms. Bacteria exploit several strategies to evade recognition by the immune system in order to survive within the host. An important strategy of bacteria is the secretion of proteins that block crucial functions of the immune system either by binding or degradation of host proteins. The gram-negative bacterium Pseudomonas aeruginosa (P. aeruginosa) causes chronic infections in patients with cystic fibrosis and immunocompromised patients. In this thesis new bacterial proteins and strategies of P. aeruginosa are described that interfere with recognition and activation of the innate immune system. Alkaline protease of P. aeruginosa degrades the ligand for Toll-like receptor 5 (TLR5) and blocks two out of three activation pathways of the complement system. TLR5 recognizes flagellin, the building block of the bacterial flagellum. This propeller-like structure is essential for bacterial motility and consists of flagellin polymers. Alkaline protease degrades TLR5-activating monomeric flagellin, in contrast to the polymeric form of flagellin, which is necessary for bacterial motility. In addition to mammals, plants have a similar flagellin sensing system via the receptor FLS2, which activation is inhibited via the same mechanism by alkaline protease. In this way, alkaline protease blocks flagellin sensing in both mammals and plants, while bacterial motility is maintained. Analysis of the complement inhibiting activity of alkaline protease resulted in the identification of complement C2 as another target of this protease. C2 plays an essential role in activation of the classical (recognition of antigen-antibody complexes) and lectin (recognition of bacterial sugar structures) pathway. Degradation of C2 by alkaline protease blocks both pathways and all downstream effects, such as recruitment of inflammatory cells to the site of infection, phagocytosis, and killing of bacteria. Since alkaline protease blocks crucial functions of the innate immune system, inhibition of this protease may be of therapeutic interest. We identified amino acids in the main body of alkaline protease inhibitor that are important for its inhibitory activity. Besides the already known alkaline protease, we describe a new protease of P. aeruginosa. This secreted protease degrades cellular receptors of white blood cells that are involved in cell adhesion and migration. We named this new protease immunomodulating metalloprotease of P. aeruginosa (IMPa). Alkaline protease and IMPa both from P. aeruginosa modulates crucial functions of the innate immune system. Studying the role of these proteases in vivo is important to understand Pseudomonas infections and to develop new therapeutic strategies.