Objective: To establish a system for notifying adverse effects (AE) at the Dos de Mayo National Hospital. Method: We performed an operative investigation of the implementation of a confidential, voluntary reporting system with active surveillance from 1 October 2005 to 31 March 2006. A systems-based model was used for the management of AE. Results: Among a total of 8,964 hospital admissions, 347 AE were reported. The rate of AE was 3.9% and there were 12 near misses (0.13%). The most frequent AE were nosocomial infections 241 (70%). The highest number of cases (47 [19.5%]) occurred in the neonatology department and the most frequent condition was neonatal sepsis (19 cases). The second most frequent AE were adverse drug reactions, amounting to 49 cases (14.2%). Of these, 39 (79.6%) were caused by antiretroviral therapy. Almost all notifications were obtained by active surveillance and there were only five voluntary reports. We found additional information in fragmented subsystems such as the nosocomial infections board, blood surveillance, pharmacology surveillance, the complaints system and audits. In addition, we searched for AE in non-elective surgical re-interventions. All AE were classified by frequency and impact. Conclusions: The estimated overall rate of AE (3.9%) was lower than that in developed countries with better health conditions, suggesting a possible under-reporting bias. We infer that active surveillance of AE coupled with integration of subsystems is currently the most appropriate way to obtain information on AE.