The measurement of thoracic electrical bioimpedance (TEB) offers a continuous, non-invasive method for monitoring cardiac output (CO). For clinical use, agreement with a current standard should be demonstrated. We describe a modification to the manufacturer's suggested data entry into the NCCOM3-R6 TEB monitor (BoMed Medical Manufacturing), which results in improved agreement with indocyanine green dye dilution (DD) CO estimation in paediatric patients. The manufacturer's instructions for the NCCOM3-R6 include an estimation of the volume of electrically participating thoracic tissue (VEPT) based on body weight. We also estimated the VEPT from direct anatomical measurement of thoracic length and circumference. The mean difference between paired DD and TEB CO using the manufacturer's weight-based instructions was 0.69 l/min with 95% confidence limits 2.34 to -0.96 l/min. The mean difference between the two CO techniques using our calculated VEPT was 0.35 l/min with 95% confidence limits 1.50 to -0.80 l/min. The linear regression correlation coefficient between the two techniques was 0.88 using VEPT estimated from the manufacturer's instructions and 0.94 using our calculated VEPT from measurement of thoracic dimensions. The range of DD CO was 0.41 to 8.35 l/min.