In the last years the zebrafish embryo has been suggested as an ideal model for cardiac research. The overall similarity between zebrafish and human in response to cardiotoxic drugs was demonstrated, for example, in drug-induced cardiac arrhythmia. For this reason, several methods have been developed to assess cardiac rate (CR) in zebrafish embryos. In this study, we present a simple, not invasive method that adopts (1) confocal microscopy (CM) image recordings of the embryo’s heart combined with (2) image processing, and (3) spectral analysis to measure the CR of zebrafish embryos.