Septic shock is a serious medical condition. With increased concerns about invasive techniques, a number of non-invasive and semi-invasive devices measuring cardiac output (CO) have become commercially available. The aim of the present study was to determine the accuracy, precision and trending abilities of the FloTrac and the continuous pulmonary artery catheter thermodilution technique determining CO in septic shock patients. Consecutive septic shock patients were included in two centres and CO was measured every 4 h up to 48 h by FloTrac (APCO) and by pulmonary artery catheter (PAC) using the continuous (CCO) and intermittent (ICO) technique. Forty-seven septic shock patients with 326 matched sets of APCO, CCO and ICO data were available for analysis. Bland and Altman analysis revealed a mean bias ±2 SD of 0.0 ± 2.14 L min−1 for APCO–ICO (%error = 34.5 %) and 0.23 ± 2.55 L min−1 for CCO–ICO (%error = 40.4 %). Trend analysis showed a concordance of 85 and 81 % for APCO and CCO, respectively. In contrast to CCO, APCO was influenced by systemic vascular resistance and by mean arterial pressure. In septic shock patients, APCO measurements assessed by FloTrac but also the established CCO measurements using the PAC did not meet the currently accepted statistical criteria indicating acceptable clinical performance.