Background <p>Emergency General Surgery (EGS) patients are clinically complex and frequently underreported, particularly in Latin America, which hampers benchmarking and quality-improvement efforts. We implemented a hospital-based structured data collection system to characterize EGS patients and outcomes in a tertiary university hospital.</p> Methods <p>We conducted a retrospective cross-sectional study of a prospectively collected database including all patients aged ≥ 13 years who required emergency general surgery between May and November 2020 at a high-complexity public university hospital in Costa Rica, comparable to a US Level I trauma center. Sociodemographic, perioperative, and outcome variables were collected. Descriptive statistics were computed. Univariate analyses and multivariable Firth penalized logistic regression were performed to identify factors independently associated with in-hospital mortality.</p> Results <p>A total of 575 patients were included; 52.9% were male and the most frequent age group was 18–29 years (23.7%). Most procedures occurred outside ordinary hours (72.2%), and surgical residents were the primary surgeons in 51.1% of cases. Laparoscopy was the initial approach in 67.8%. The most frequent care categories were gastrointestinal emergencies (48.2%), hepatobiliary emergencies (23.7%), and trauma (8.2%). Acute appendicitis (37.4%) and gallbladder and biliary disease (23.3%) were the leading diagnostic groups. Overall in-hospital mortality was 5.6%. In the final complete-case cohort (<i>n</i> = 511), mechanical ventilation, ASA III-IV status, hemodynamic instability, and open abdomen were independently associated with in-hospital mortality.</p> Conclusions <p>These findings provide a contemporary description of emergency general surgery patients treated at a Latin American tertiary-care hospital and identify clinical factors associated with in-hospital mortality.</p> Trial registration <p>NCT05930574</p>