Antithrombin is a key endogenous anticoagulant that also plays other roles in inflammation, immunity, and other processes. Congenital antithrombin deficiency is the most severe type of thrombophilia, yet characterized by a remarkable clinical heterogeneity. Here, as a primer for internists, we present a practical review of data regarding this disorder, focused on its molecular basis, diagnostic procedures, prognostic implications, and clinical management of patients suffering from this severe, and probably underdiagnosed, type of thrombophilia.