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Background The Physiological and Operative Severity Score for enUmeration of Morbidity and Mortality (POSSUM) and its Portsmouth modification (P-POSSUM) were developed for comparative audit in surgical patients. This study evaluated applicability of these systems in estimating mortality and morbidity risks in a cohort of patients undergoing laparotomy at the national referral hospital in Nairobi, Kenya. Methods Data of 166 patients undergoing laparotomy was subjected to POSSUM and P-POSSUM scoring systems and analyzed using linear and exponential methods. The discrimination power of POSSUM and P-POSSUM as predictors of surgical outcome was measured using the receiver–operating characteristic (ROC) curve. Results The overall observed to expected (O:E) ratio using linear analysis was 0.29:1 (POSSUM) and 0.67:1 (P-POSSUM) while exponential analysis gave an O:E of 0.2:1 (POSSUM) and 0.4:1 (P-POSSUM). The predicted morbidity using POSSUM was 1.09:1 (linear analysis) and 1:1 (exponential analysis). Hosmer–Lemeshow analysis did not show a significant lack of fit with the observed mortality when applied to POSSUM and P-POSSUM. The area under ROC curve was 0.74 (POSSUM) and 0.78 (P-POSSUM). Conclusion Our results support the suitability of P-POSSUM and POSSUM scoring systems to stratify morbidity and mortality risk in our study population.