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Development of drugs requires electrophysiological studies of small animals like mice, rats or guinea pigs. Electrocardiography (ECG) of hirsute animals is time-consuming. We have developed a micro magnetometer array with a 9-channel superconducting quantum interference device (SQUID) with a 2.5-mm diameter pickup-coil for noncontacting measurement of magnetocardiograms (MCGs) in small animals. The micro-MCG successfully recorded the PQRST complex in mice, rats and guinea pigs. A regional myocardial injury was made in rat hearts with a cryoinjury probe, and the characteristic pattern of the injury was recorded in the MCG. An anterior myocardial injury created a QS pattern in the MCG, and a posterior myocardial injury created a QR pattern in the MCG. Quinidine-induced QT prolongation was successfully detected by micro-MCG in mice and rats. Simultaneous recording of ECG and MCG was conducted after intraperitoneal administration of quinidine (60 mg/kg) in guinea pigs. QT interval corrected for heart rate (QTc) in both ECG and MCG correlated well. The newly developed micro-MCG may facilitate electrophysiological studies of small animals, and may enable high-throughput screening of drug-induced QT abnormality.