The study aims to highlight the usefulness of micro accounting approach as tool of clinical governance starting from the data provided by the computerization of services and medical records. The case study takes into account data collected over two years between three departments of the same hospital for the management of patients with acute gastric ulcer with bleeding and variations and acute duodenal ulcer with bleeding and variations. All statistical analyses were performed using STATA V.14.2 (Stata Corp, College Station, Texas, USA, 2013) and p value <0.05 was considered significant for all analyses. The analysis of economic and comorbidity data provides useful insights to guide the choice of the treatment pathway between departments, and provides useful indications for the redefinition of guidelines towards a rationalization of healthcare expenditure.