In order to perform in vitro cardiotoxicity screening of pharmacological substances, multi-electrode array systems are increasingly used to measure the extracellular field potentials of cell layers of human induced pluripotent stem cell cardiomyocytes. The analysis of the field potentials is usually performed using complex analysis software provided by the hardware manufacturers. In the case of the Cardiac Analysis Tool software from Axion Biosystems, inconsistencies were found in the results, which can significantly influence the cardiotoxicity screening results. In order to obtain more reliable results, a new algorithm was developed and implemented in an easy-to-use software tool, the INCardio Data Analysis Tool, which, due to its high degree of automation, can also be used by inexperienced users. The validation reveals differences in the results of the two tools both in depolarization spike amplitudes and in the time course of the field potential durations. The manual analysis of all signals affected by deviations shows that the results of the newly developed Data Analysis Tool are correct in all cases and can therefore be classified as more accurate and reliable than the reference analysis software.