In order to investigate quantitatively and objectively the influence of the normal microbial flora on the ultrastructure of the alveolar macrophage, three groups of mice were studied stereologically: germ-free (GF), conventionally reared under non sterile isolation conditions (IC), and conventionally reared in an open environment (OC). The alveolar macrophages of GF mice possess a smaller mitochondrial compartment, possibly with fewer organelles, than the macrophages of conventional mice. Other influences of the normal microflora on alveolar macrophage substructure are obscured by the effects of nonmicrobial stimuli such as droplets of lung surfactant. No previous comparison exists of alveolar and peritoneal macrophage ultrastructure. Lung macrophages are larger than the phagocytes of the peritoneum, but the difference in size is much less than is commonly believed. Alveolar macrophages are rounder than peritoneal macrophages, and exhibit much less rough endoplasmic reticulum (RER) as well as differences in mitochondrial morphometry. No difference in mitochondrial volume fraction exists between the two types of macrophage even though alveolar macrophages represent the extreme of aerobic adaptation in the mononuclear phagocyte system. Phagosomes occupy a significant fraction of cellular volume only in the alveolar macrophages. Moreover alveolar phagocytes contain fewer but larger represent the first objective, quantitative structural evidence confirming the common belief that alveolar macrophages experience greater physiological stimulation than peritoneal macrophages. The normal microflora accounts for only a small proportion of the differing degree of stimulation exerted on the two types of macrophage.