In 430 BC, a plague struck the city of Athens, which was then under siege by Sparta during the Peloponnesian War (431-404 BC). In the next 3 years, most of the population was infected, and perhaps as many as 75,000 to 100,000 people, 25% of the city's population, died. The Athenian general and historian Thucydides left an eye-witness account of this plague and a detailed description to allow future generations to identify the disease should it break out again. Because of the importance of Thucydides and Athens in Western history and culture, the Plague of Athens has taken a prominent position in the history of the West for the past 2500 years. Despite Thucydides' careful description, in the past 100 years, scholars and physicians have disagreed about the identification of the disease. Based on clinical symptoms, 2 diagnoses have dominated the modern literature on the Athenian plague: smallpox and typhus. New methodologies, including forensic anthropology, demography, epidemiology, and paleopathogy, including DNA analysis, have shed new light on the problem. Mathematical modeling has allowed the examination of the infection and attack rates and the determination of how long it takes a disease to spread in a city and how long it remains endemic. The highly contagious epidemic exhibited a pustular rash, high fever, and diarrhea. Originating in Ethiopia, it spread throughout the Mediterranean. It spared no segment of the population, including the statesman Pericles. The epidemic broke in early May 430 BC, with another wave in the summer of 428 BC and in the winter of 427-426 BC, and lasted 4.5 to 5 years. Thucydides portrays a virgin soil epidemic with a high attack rate and an unvarying course in persons of different ages, sexes, and nationalities.The epidemiological analysis excludes common source diseases and most respiratory diseases. The plague can be limited to either a reservoir diseases (zoonotic or vector-borne) or one of the respiratory diseases associated with an unusual means of persistence, either environmental/fomite persistence or adaptation to indolent transmission among dispersed rural populations. The first category includes typhus, arboviral diseases, and plague, and the second category includes smallpox. Both measles and explosive streptococcal disease appear to be much less likely candidates.In 2001, a mass grave was discovered that belonged to the plague years. Ancient microbial typhoid (Salmonella enterica serovar Typhi) DNA was extracted from 3 skeletons. Because typhoid was endemic in the Greek world, it is not the likely cause of this sudden epidemic. Mt Sinai J Med 76:456-467, 2009. (c) 2009 Mount Sinai School of Medicine.