In 25 anesthetized, intubated, artificially ventilated, and paralyzed healthy neonates and infants, end-tidal PCO2 (PETCO2) measured by remote multiplexed mass spectrometry was 1.86 +/- 1.58 mm Hg lower than arterial PCO2 (PaCO2). PETCO2 measured by a flow-through cuvette was 1.02 +/- 1.64 mm Hg lower than PaCO2. The difference between the two methods of capnography was not significant. Values for PETCO2 obtained by mass spectrometry changed -0.43 +/- 1.43 mm Hg from baseline after 15 minutes of aspiration at a sample flow rate of 240 ml/min. Values for PETCO2 obtained with flow-through capnography changed -0.17 +/- 2.17 mm Hg from baseline after 15 minutes. In both methods, the changes from baseline in PETCO2 over time were not significant. These results suggest that both methods of capnography studied are reliable and may be used safely in neonates despite high sample flow rates and added apparatus dead space (0.6 ml for tracheal tubes less than or equal to 4.0 mm OD and 4.9 ml for tracheal tubes greater than 4.0 mm OD).