Primary pneumonia is caused by the patient's inhaling or aspirating a pathogen such as bacteria or a virus. Bacterial pneumonia, often caused by staphylococcus, streptococcus, or klebsiella, usually occurs when the lungs' defense mechanisms are impaired by such factors as suppressed cough reflex, decreased cilia action, decreased activity of phagocytic cells, and the accumulation of secretions. Viral pathogens account for up to a fourth of CAPs in adults and are most commonly caused by the influenza virus. Viral pneumonia occurs when a virus attacks bronchiolar epithelial cells and causes interstitial inflammation and desquamation, which eventually spread to the alveoli. In addition to the influenza viruses mentioned above, other common viruses include respiratory syncytial virus (RSV); influenza A; parainfluenza 1, 2, and 3; and adenovirus.

Secondary pneumonia ensues from lung damage that was caused by the spread of bacteria from an infection elsewhere in the body or by a noxious chemical. Aspiration pneumonia is caused by the patient's inhaling foreign matter such as food or vomitus into the bronchi. Factors associated with aspiration pneumonia include old age, impaired gag reflex, surgical procedures, debilitating disease, and decreased level of consciousness.

CAP is caused by bacteria that are divided into two groups: typical and atypical. Organisms that cause typical pneumonia include Streptococcus pneumoniae (pneumococcus) and Haemophilus and Staphylococcus species. Organisms that cause atypical pneumonia include Legionella, Mycoplasma, and Chlamydia species.