The validity of each new cardiac output (CO) monitor should be established before implementation in clinical practice. For this purpose, method comparison studies investigate the accuracy and precision against a reference technique. With the emergence of continuous CO monitors, the ability to detect changes in CO, in addition to its absolute value, has gained interest. Therefore, method comparison studies increasingly include assessment of trending ability in the data analysis. A number of methodological challenges arise in method comparison research with respect to the application of Bland–Altman and trending analysis. Failure to face these methodological challenges will lead to misinterpretation and erroneous conclusions. We therefore review the basic principles and pitfalls of Bland–Altman analysis in method comparison studies concerning new CO monitors. In addition, the concept of clinical concordance is introduced to evaluate trending ability from a clinical perspective. The primary scope of this review is to provide a complete overview of the pitfalls in CO method comparison research, whereas other publications focused on a single aspect of the study design or data analysis. This leads to a stepwise approach and checklist for a complete data analysis and data representation.