Histamine is a biogenic amine with extensive effects on many immune cell types. Histamine and its four receptors (H1R-H4R) represent a complex system of immunoregulation with distinct effects dependent on receptor subtypes and their differential expression. In addition to mammalian cells, bacteria can also secrete histamine and the influence of microbiota-derived histamine on host immunological processes is only beginning to be described. However, it is clear that histamine-secreting microbes are present within the human gut microbiota and their levels are increased in asthma patients. Additional studies are required to fully understand the complex regulatory interactions between histamine and the host immune response to everyday microbial and environmental challenges.