We have fabricated a high-Tc SQUID magnetometer to measure magnetocardiographic signals from small animals, aiming to use the magnetometer in a basic physiological study of cardiac functions. Two directly coupled SQUIDs were located with a vertical spacing of 8.5cm and formed a direct-feedback gradiometer. The SQUID system was operated within a magnetically shielded room having an attenuation of 50 dB at low frequencies. Due to a small gap of 3 mm of the dewar tail, relatively large signal of up 40 pT in peak to peak of rats’ MCG was detected. Using the SQUID system, pilot study on the change of the fluctuation of heart rate after artificial myocardial dysfunction of rats has been made, where animal models of acute myocardial infarction were prepared by the ligation of coronary artery. Repeated measurements of the heart rate were made during 4 weeks after the infarction. The results of the R-R intervals were analyzed in terms of low- and high-frequency components, from which the variation of the activities of autonomic nervous system was estimated.