Introduction: Right heart catheterization (RHC) is a diagnostic procedure, the main purpose of which is to diagnose pulmonary hypertension and investigate its etiology and treatability. In addition to measuring blood pressure in heart chambers, it includes estimating cardiac output (CO) and calculation of pulmonary vascular resistance (PVR) derived from the CO. There are two common methods to evaluate the CO—the indirect Fick method and the thermodilution method. Depending on the clinical conditions, either of the two may be considered better. Several studies have showed that, in most cases, there is no difference between measurements rendered by the two methods. Other studies have raised suspicion of a discrepancy between the two methods in a substantial number of patients. A clear opinion on this matter is missing. Aim: To evaluate the agreement between the values of the CO and PVR found by the thermodilution and indirect Fick methods. Methods: We retrospectively included patients that underwent RHC in Kaplan Medical Center during the last two years with a measurement of the CO using both the thermodilution and the indirect Fick methods. The measurements obtained upon RHC and the clinical data of the patients were collected. The values of the CO and PVR measured or calculated using the two methods were compared for each patient. Results: We included 55 patients that met the inclusion criteria in this study. The mean CO measured by the thermodilution method was 4.94 ± 1.17 L/min and the mean CO measured by the indirect Fick method was 5.82 ± 1.97 L/min. The mean PVR calculated using the thermodilution method was 3.33 ± 3.04 Woods’ units (WU) and the mean PVR calculated using the indirect Fick method was 2.71 ± 2.76 WU. Among the patients with normal mPAP, there was a strong and statistically significant correlation between the PVR values calculated by the two methods (Peasron’s R2 = 0.78, p-value = 0.004), while among the patients with elevated mPAP, the correlation between the PVR values calculated by the two methods was not statistically significant. Conclusion: The findings of this small study demonstrate that, in a proportion of patients, the indirect Fick method and thermodilution method classify the PVR value differently. In our experience, it seems that, in these patients, the indirect Fick method misclassified patients with a pathological finding as normal. We, therefore, recommend that upon performing RHC, at least in patients with mPAP > 25 mmHg, both the thermodilution and indirect Fick methods be performed and, whenever they disagree, the values obtained from the thermodilution method should be preferred.