Pulmonary alveolar macrophages (PAMa) are located in the alveoli of the lungs and protect the respiratory tract against respiratory pathogens. PAMa are the main phagocytes of the innate immune system and they originate from the yolk sac. Functionally, PAMa are tasked with maintaining pulmonary homeostasis and protecting the body from invading pathogens. Importantly, they also control the response to pathogens and epithelial damage, use phagocytosis to remove apoptotic cells, and remove waste material from the epithelium. PAMa have two functional states known as the M1 phenotype and the M2 phenotype. The function of M1 macrophages is to recruit immune cells into the lung. Conversely, M2 macrophages secrete factors which reduce inflammation and stimulate repair in the epithelium. In order to identify pathogens and injury sites, PAMa have pattern recognition receptors, such as toll-like recepetors. Additionally, PAMa are known to express angiotensin-converting enzyme 2 (ACE2), making them a potential alternative route for infection from pathogens such as SARS-CoV-2. The infection of alveolar macrophages by SARS-CoV-2 may also promote the cytokine storm which occurs in severe COVID-19 patients. Rat PAMa (RPAMa) can be used to study pulmonary disease and better understand the role these cells play in lung disease tolerance.