Rodent lungs are routinely examined after intratracheal instillation (IT) of fixative. This study compares the histopathologic appearance of the lung after IT fixation with air inflation (AI) followed by immersion fixation. Lungs from mice chronically exposed to cigarette smoke were fixed either by IT or by AI. Increased numbers of macrophages with differing distributions were seen in both groups. Lungs fixed by IT had prominent, large macrophages floating in the alveolar lumina, as well as macrophage clusters and loose aggregates, often near terminal airways. Macrophages in lungs fixed by AI were randomly distributed throughout the lung, lying singly along alveolar walls, with large numbers visible in the interstitium. Clusters of macrophages were seen in the airways after AI but were fewer after IT fixation. The effects of intratracheal fixation on lung macrophages need to be considered carefully when assessing the significance of changes in macrophage appearance and distribution.