PURPOSE: We aimed to test the convergent validity of the COMFORT scale and the Cardiac Analgesic Assessment Scale (CAAS) and to evaluate changes in physiological parameters over time in response to a painful procedure in neonates and infants following cardiac surgery. METHODS: From October 2006 to May 2008, 16 children were prospectively evaluated over 1-3 days after cardiac surgery while they remained on mechanical ventilation and received infusions of sedatives and analgesics. Pain was assessed by the COMFORT scale and CAAS before and during endotracheal tube suctioning. Heart rate, systemic systolic blood pressure, pulmonary artery pressure, oxygen saturation and pupil size were recorded at the same times. RESULTS: During endotracheal suctioning on the first day, there was a significant increase in COMFORT and CAAS scores, systemic systolic blood pressure tended to decrease, pulmonary artery pressure significantly increased and there was a significant reduction in oxygen saturation. Heart rate and pupil size did not change significantly during the painful procedure throughout the study. COMFORT scores significantly correlated with CAAS scores on all days. Nevertheless, agreement for the detection of pain between both scales was weak (kappa<0.5). The COMFORT scale detected more patients with pain. CONCLUSIONS: There was poor agreement between the COMFORT scale and CAAS for detection of pain in neonates and infants who had undergone cardiac surgery. A reduction in systemic systolic blood pressure and a rise in pulmonary artery pressure were observed during painful stimulation on the first post-operative day. For this population, a pain scale scoring physiological parameters according to their variation to higher and lower values should be developed.