The innate immune system is the first line of defense against pathogenic microorganisms, such as bacteria, fungi, and viruses. Phagocytes, such as neutrophils and macrophages, play an important role in the innate immune system by recognizing, engulfing, and eliminating pathogens. It has been suggested that lipid membrane microdomains/rafts of phagocytes are involved in these innate immune responses, including superoxide generation, cell migration, and phagocytosis. Lactosylceramide (LacCer), a neutral glycosphingolipid, forms glycosphingolipid-enriched microdomains together with the Src family kinase, Lyn, on the neutrophil plasma membrane. LacCer-enriched microdomains have been suggested to play important roles in innate immune function of neutrophils. However, the molecular mechanisms underlying these phenomena remain largely unknown. Recent proteomic analyses of microdomains from phagocytes have provided insight into membrane microdomain-mediated functions in the processes of phagocytosis. In this review, we discuss the membrane microdomain-associated immune functions of phagocytes, focusing on those functions of LacCer-enriched microdomains and recent proteomic approaches to determine the molecular mechanisms underlying these functions.