The purpose of this study was to measure organ doses and the effective dose (ED) using a three-dimensional rotational X-ray (3D-RX) system and to determine the ED conversion factor from the dose area product (DAP) for skull, spine and biliary protocols. A commercial 3D-RX imaging system was used to simulate the protocols with the adult female anthropomorphic phantom. Twenty MOSFET detectors were used to measure the absorbed doses at various organ locations. The ED was calculated for each protocol and the corresponding DAP was obtained. The skin dose was the highest for all the protocols. The second highest organ doses were those of the brain for the skull, the intestine for the spine and the kidney for the biliary protocol. The ED was 0.4-0.9, 4.2-8.4 and 3.2-4.6 mSv, and the ED conversion factor was 0.06-0.09, 0.18-0.31 and 0.13-0.23 mSv Gy(-1) cm(-2) for each protocol, respectively. This data may be used to estimate the patient ED for those protocols in the 3D-RX.