Innate immunity is the first and in most organisms sole line of defence against pathogenic microorganisms. The activity of mechanisms of innate immunity starts with recognition of pathogen- associated molecular pattern (PAMP) by proteins that contain leucine rich repeats (LRR) domain. Plant proteins ‘R’ contain TIR, NBD and LRR domains and recognize specifically fungal, bacterial or viral pathogens. After pathogen detection signal cascade is initiated that results in most cases with hypersen- sitive reaction in region of infection. In animals Toll-like receptors are best described PAMP-recognizing molecules to date. With its extracellular LRR domain they can bind pathogen-derived molecules but also molecules that are produced by host organism during infection. Such interaction leads to immunic reaction: production of chemokins, cytokines, regulators of transcription, translation and proteolytic processes or synthesis of secretional proteins including these belonging to complement system. NOD proteins are recently discovered mammalian intracellular PAMP receptors that resembles plant ‘R’ proteins by its domain structure. They recognize components of bacterial cell wall and trigger inflammatory reaction by activation of nuclear factor (NF-κB). Mutations in NOD protein NOD2 has been found to be related to Crohn disease, early onset sarcoidosis, Blau syndrom and certain types of cancer.