The early organism response to injury or infection involves activation of the innate immune system, in which pattern recognition receptors (PRRs) participate. They recognize highly conservative structures that are called pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs). The interactions between PRRs and PAMPs or DAMPs lead to the activation of transcriptional factors which are responsible for gene expression of inflammatory mediators and synthesis and release of these factors, and result in the development of inflammation. RAGE (receptor for advanced glycation end products) and CD163 belonging to PRRs play a significant role in the early immune response in lungs. They are expressed on alveolar epithelial cells and alveolar macrophages, respectively. NK cells are also involved in lung response to injury, though their maturation and the ability to express PRRs depend on the presence of IL-15. Detailed knowledge about these factors enables us to understand the signal pathways that are activated in the course of infectious and noninfectious lung injury. The analysis of these proteins’ concentrations in body fluids creates new possibilities in monitoring lung injury and predicting the results of treatment. In the future, the discussed mediators may become the targets for new forms of treatment in life-threatening respiratory diseases.