To obtain phagocytosis at the site of microorganism invasion implies recruitment of cells via chemoattraction. In vertebrates, this can be done by several categories of molecules such as proinflammatory chemokines/cytokines or the complement fragments C3a and C5a (in the following section, C3a fragments like in mammals may be found in tunicates but not in other non-vertebrates; yet, C3 may be cleaved in different ways in the invertebrates). C3b, mannose-binding lectin (MBL), and many other lectins can function as opsonins.

Ingestion follows phagocytosis, and then killing occurs by an oxidative mechanism with the production of ROS and nitric oxide (NO). These mechanisms are conserved in phylogeny. Unique to all gnathostomes(有颌), activation of phagocytes also leads to upregulation of antigen processing machinery, costimulatory molecules, and proinflammatory cytokines to enhance adaptive immunity. Phagocytosis can also be performed by B cells, as described below.