The rapidly increasing number of diagnostic computed tomography (CT) procedures in the recent decades has spurred heightened concern over the potential risk to patients. Although an accurate organ dose assessment tool has now become highly desirable, existing software packages depend on stylized computational phantoms that were originally developed more than 40 years ago, exhibiting very large discrepancies when compared with phantoms that are anatomically realistic. However, past comparative studies did not focus on CT protocols for adult patients. This study was designed to quantitatively compare two types of phantoms, the stylized phantoms and a pair of recently developed RPI-adult male and adult female (RPI-AM and RPI-AF) phantoms, for various CT scanning protocols involving the chest, abdomen-pelvis and chest-abdomen-pelvis. Organ doses were based on Monte Carlo simulations using the MCNPX code and a detailed CT scanner model for the GE LightSpeed 16. Results are presented as ratios of organ doses from the stylized phantoms to those from the RPI phantoms. It is found that, for most organs contained in the scan volume, the ratios were within the range of 0.75-1.16. However, the stomach doses are significantly different and the ratio is found to be up to 1.86 in male phantoms and 2.29 in the female phantoms due to the anatomical differences between the two types of phantoms. Organs that lie near a scan boundary also exhibit a significant relative difference in organ doses between the two types of phantoms. This study concludes that, due to relatively low x-ray energies, CT doses are very sensitive to organ shape, size and position, and thus anatomically realistic phantoms should be used to avoid the dose uncertainties caused by the lack of anatomical realism. The new phantoms, such as the RPI-AM and AF phantoms that are designed using advanced surface meshes, are deformable and will make it possible to match the anatomy of a specific patient leading to further improvement in dose and risk assessments for patients undergoing CT examinations.