Coronary artery CT angiography has short scanning length, the exposure dose is high. Therefore, it is required to study on the organ dose when using MDCT. We compared the differences between the absorbed dose and effective dose in the major organs assessing the absorbed dose in the major organs by 16-MDCT and 64-MDCT in the subjects with coronary artery CT angiography, the same protocol by 16-MDCT and 64-MDCT. As a result, the great orders of absorbed dose when conducting coronary artery CT angiography had been shown as heart, stomach, liver, pancreas, kidney, spleen, large intestine, lung, small intestine, thyroid gland, ovary, bladder, and orbit with the absorbed dose distribution of $0.538{\pm}0.026(Mean{\pm}SD,\;p<0.05)mGy{\sim}71.316{\pm}4.316mGy$ in 16-MDCT, and heart, stomach, pancreas, spleen, liver, kidney, small intestine, large intestine, lung, thyroid gland, ovary, bladder, and orbit with the absorbed dose distribution of $0.87{\pm}0.01mGy{\sim}115.26{\pm}1.59mGy$ in 64-MDCT, demonstrating some different distributions. The exposed doses to the patient per one time scanning with coronary artery CT angiography were $71.316{\pm}4.316mGy$ in 16-MDCT as the absorbed dose based on the heart and $115.26{\pm}1.59mGy$ in 64-MDCT. The effective doses were 7.41 mSv and 12.11 mSv in 16 and 64-MDCT, respectively. Taking into account the results of brain CT with 2.8 mSv that has comparatively large scanning length and size, facial CT 0.8 mSv, chest CT 5.7 mSv, pelvic CT 7.2 mSv, and abdominal and pelvic CT 14.4 mSv, it is very high considering the scanning length of 13 cm limited to the heart for the scanning range.