Objective: To study the effect of using an Intensive Care Information System (ICIS) on severity scores and prognostic indices: Acute Physiology and Chronic Health Evaluation II (APACHE II), Simplified Acute Physiology Score II (SAPS II), and Mortality Probability Models II (MPM II). Design: Prospective pilot study. Setting: A 20-bed medical-surgical intensive care unit (ICU) in a teaching hospital. Patients: 50 consecutive adult patients admitted to the ICU on a bed equipped with an ICIS. Interventions: None. Measurements and results: In each patient all the physiologic variables, as required by the severity scores, were both manually charted and recorded by ICIS. ICIS registration resulted in the extraction of more abnormal values for all physiologic variables (except temperature): p < 0.05. Higher severity scores and mortality prediction were achieved by using ICIS charting: predicted mortality increased by 15% for APACHE II compared to manual charting, 25% for SAPS II, and 24% for MPM0. ICIS charting resulted in higher severity scores and mortality prediction for 29 of the 50 patients using APACHE II with a mean increase in mortality prediction in this subgroup of 27%. In the case of SAPS II, ICIS charting resulted in higher scores in 23 of the 50 patients and in the case of MPM0 in 13 patients, the mean increase in mortality in these subgroups being 64 and 148%, respectively. Conclusions: The use of ICIS charting to acquire the most abnormal physiologic values for severity scores and the derived prognostic indices results in a higher mortality prediction. Comparison of groups of patients and/or ICUs based on severity scores is impossible without standardization of data collection. The mortality prediction models have to be revalidated for the use of ICIS charting. While awaiting this, we suggest that every patient record in local regional, national, or international ICU databases should be marked as being recorded by manual or by ICIS charting.