Tools to accurately estimate the risk of death following emergency surgery are useful adjuncts to informed consent and clinical decisions. This prospective study compared the Physiological and Operative Severity Score for the Enumeration of Mortality and Morbidity (POSSUM) and Portsmouth POSSUM (P-POSSUM) scoring systems with clinical judgement in predicting mortality from emergency surgery. Data were collected prospectively from 163 patients. Details of the physiological and operative severity scores were recorded for POSSUM and P-POSSUM. The estimates of both the surgeon and anaesthetist for 30-day and in-hospital mortality were also recorded pre-operatively. The accuracies of the four predictions were then compared with actual mortalities using linear and exponential analysis and receiver operator characteristics (ROC). P-POSSUM gave the most accurate prediction of 30-day mortality using linear analysis [observed to expected ratio (O : E) = 1.0]. POSSUM gave the most accurate prediction using exponential analysis (O : E = 1.15). Clinical judgement of mortality from both operating surgeons and anaesthetists compared favourably with the scoring systems for 30-day mortality (O : E = 0.83 and O : E = 0.93, respectively). ROC analyses showed both clinical judgement and the POSSUM scores to be good predictors of 30-day mortality with area under the curve values (AUC) of 0.903, 0.907, 0.946 and 0.940 for surgeons, anaesthetists, POSSUM and P-POSSUM respectively. POSSUM and P-POSSUM appear to be useful indicators for the prediction of mortality. Clinical judgement compares strongly with scoring systems in predicting post-operative mortality, but may underestimate mortality in very high-risk patients with more than 90% mortality.