Cardiac arrhythmia is considered important cause of cardiovascular disorder in birds. Little is known, however, about arrhythmia during embryonic stages, chiefly because of their relative rarity and difficulty in diagnosis. Electrocardiogram (ECG) can't be applied in avian samples non-destructively due to the eggshell. Therefore, an alternative method is an important tool if avian or reptilian embryo research in this area is to advance. Here, we addressed, a non-invasive method to diagnosis cardiac arrhythmia based on optical sensor together with signal processing. In such a system, the intensity of transmitted light is mostly affected by pulsatile blood volumes and mechanical activity of the heart during blood pumping. In our measurement procedure, the time domain transmissive signal was transformed into the frequency domain using fast Fourier transform (FFT). We interpreted the cardiac signal of embryo with a naturally occurred bradycardia throughout the incubation. We found a normal heart rate (HR) during first half of incubation, but HR had two frequency components in the mid incubation and finally a much lower frequency heart rate up until hatching. Early detection of potentially abnormal chicks with cardiovascular defects could significantly contribute to the humane treatment of these embryos and increase production efficiencies by identifying high quality embryos. Moreover, this method could be used in developmental physiology, and cardiovascular medicine research in avian and reptile protocols in the future.