Systemic lupus erythematosus (SLE) is considered the archetypal systemic autoimmune disease. Clinically characterized by multisystem involvement and varied serologic abnormalities, no two patients present or have disease that evolves in exactly the same way. Viewed histologically, SLE is characterized by some combination of inflammation and fibrosis, and the clinical phenotype is dictated by the relative contributions of each and the organs affected. Tissue injury appears to be mediated by characteristic autoantibody production, immune complex formation, and their organ-specific deposition. As expected in a multisystem disease, the entire pulmonary system is vulnerable to injury. Any of its compartments—airways, lung parenchyma, vasculature, pleura, or the respiratory musculature—may be independently or simultaneously affected. This article offers the reader a comprehensive review of the numerous pulmonary and thrombotic manifestations of SLE and suggests approaches to their management.