We measured cardiac acetylcholine (ACh) in mice using four different methods. The mice in the in vivo irradiation group received microwave irradiation and then the hearts were removed. The animals in the in vitro irradiation group were decapitated and only the hearts were irradiated. The animals in the non-frozen group were decapitated and ACh was measured soon after the removal of the heart. The animals in the frozen group were decapitated and the hearts were frozen. There were significant differences in ACh concentrations between the in vivo irradiation group and the other groups. We also measured the ACh concentrations in both atria and ventricles after the mice were irradiated while alive. The atrial ACh concentration 1.70 +/- 0.70 nmol/g (mean +/- SD) was significantly higher than the ventricle concentration 1.07 +/- 0.30. We concluded the microwave irradiation of animals was suitable method of sacrifice for the measurement of cardiac ACh.