Organ absorbed doses in computed tomography (CT) scans can be measured with anatomical phantoms but not inside the human body. In this study, a straightforward method was investigated to estimate organ doses in clinical CT using the radiation treatment planning system (RTPS) and compared them with experimental results of photoluminescence dosemeters (PLD). In a heterogeneous phantom, the average difference between PLD and RTPS values were -5.0% for the body and 7.1% for the lung. Using CT data, organ doses in 30 clinical cases were then calculated. There was a significant inverse correlation between the calculated values of organ doses and body mass index (BMI, correlation coefficients (r) = -0.69 (whole body), -0.80 (right lung), -0.81 (left lung), -0.76 (spinal cord), -0.74 (vertebra bone), -0.74 (heart), and -0.79 (oesophagus), all p < 0.01). An RTPS can be a simple and useful tool for estimating equivalent doses inside the human body, during whole-body CT scans.