Innate immunity is induced after sensing microbial components by pattern-recognition receptors and functions as a first line of host defense against microbes. However, innate immunity is also induced after sensing host-derived stimulatory substances such as monosodium urate crystals and causes the development of inflammatory diseases, such as gout. Therefore, a better understanding of innate immunity is required for the development of effective therapeutic treatments for infectious and inflammatory diseases. This paper summarizes recent findings on regulation of the innate immune response. Accumulating evidence has shown that the intracellular degradation system is critically involved in various cellular processes. We focused on the intracellular degradation system and have revealed the molecular mechanisms underlying regulation of the innate immune response. Ubiquitin-proteasome, autophagy and phagocyte-specific proteases most certainly regulate the innate immune response induced by infection of microbes and exposure to host-derived stimulatory substances. Therefore, intracellular degradation systems would be attractive therapeutic targets for the treatment of immune-related diseases.