Research on the innate immunity has accelerated over the last decades. The main reason for this has been the discovery of receptors recognizing danger molecules from pathogens. This has been facilitated through genome and transcriptome sequencing of different fish species. Also, endogenous host molecules from sterile physiological insults may also bind to certain receptors and induce immunological processes. The magnitude and quality of adaptive immunity are known to be dependent on the instructions the innate response gives. This chapter gives an overview of selected innate immune organs/tissues, factors, and processes that have been suggested to possess important roles during innate immune response in fish.