This second edition presents methods and protocols to aid readers in the design and execution of experiments used to define critical elements associated with innate immune system function. New and updated chapters detail protocols on in vitro and ex vivo studies in key cell types associated with innate immunity and with in vivo protocols used to study immune system function in the mouse. Additionally, chapters describe methods to evaluate innate immune function and new protocols associated with autism, cancer, microfluidics platforms, and CRISPR systems. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and easy to use, Mouse Models of Innate Immunity: Methods and Protocols, Second Edition will serve the research community by providing expert advice and protocols that allow both experienced and novice investigators to successfully plan, implement, and assess disease processes associated with the innate immune system.