The scarcity of suitable organ donors leads to protracted waiting times and mortality in patients awaiting lung transplantation. This study aims to assess the short- and long-term effects of a high emergency organ allocation policy on the outcome of lung transplantation. We developed a simulation model of lung transplantation waiting queues under two allocation strategies, based either on waiting time only or on additional criteria to prioritise the sickest patients. The model was informed by data from the United Network for Organ Sharing. We compared the impact of these strategies on waiting time, waiting list mortality and overall survival in various situations of organ scarcity. The impact of a high emergency allocation strategy depends largely on the organ supply. When organ supply is sufficient (>95 organs per 100 patients), it may prevent a small number of early deaths (1 year survival: 93.7% against 92.4% for waiting time only) without significant impact on waiting times or long-term survival. When the organ/recipient ratio is lower, the benefits in early mortality are larger but are counterbalanced by a dramatic increase of the size of the waiting list. Consequently, we observed a progressive increase of mortality on the waiting list (although still lower than with waiting time only), a deterioration of patients' condition at transplant and a decrease of post-transplant survival times. High emergency organ allocation is an effective strategy to reduce mortality on the waiting list, but causes a disruption of the list equilibrium that may have detrimental long-term effects in situations of significant organ scarcity.