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The recent suggestion that the late medieval Eurasian plague pandemic, the Black Death, had its origins in the thirteenth century rather than the fourteenth century has brought new scrutiny to texts reporting ‘epidemics’ in the earlier period. Evidence both from Song China and Iran suggests that plague was involved in major sieges laid by the Mongols between the 1210s and the 1250s, including the siege of Baghdad in 1258 which resulted in the fall of the Abbasid caliphate. In fact, re-examination of multiple historical accounts in the two centuries after the siege of Baghdad shows that the role of epidemic disease in the Mongol attacks was commonly known among chroniclers in Syria and Egypt, raising the question why these outbreaks have been overlooked in modern historiography of plague. The present study looks in detail at the evidence in Arabic sources for disease outbreaks after the siege of Baghdad in Iraq and its surrounding regions. We find subtle factors in the documentary record to explain why, even though plague received new scrutiny from physicians in the period, it remained a minor feature in stories about the Mongol invasion of western Asia. In contemporary understandings of the genesis of epidemics, the Mongols were not seen to have brought plague to Baghdad; they caused plague to arise by their rampant destruction. When an even bigger wave of plague struck the Islamic world in the fourteenth century, no association was made with the thirteenth-century episode. Rather, plague was now associated with the Mongol world as a whole.