In positron emission tomographic (PET) scanning, transmission measurements for attenuation correction are commonly performed by using external germanium-68 rod sources. Recently, combined PET and computed tomographic (CT) scanners have been developed in which the CT data can be used for both anatomical-metabolic image formation and attenuation correction of the PET data. The purpose of this study was to evaluate the difference between germanium- and CT-based transmission scanning in terms of their radiation doses by using the same measurement technique and to compare the doses that patients receive during brain, cardiac and whole-body scans. Measurement of absorbed doses to organs was conducted by using a Rando Alderson phantom with thermoluminescent dosimeters. Effective doses were calculated according to the guidelines in the International Commission on Radiation Protection Publication Number 60. Compared with radionuclide doses used in routine 2-[fluorine-18]-fluoro-2-deoxy-D-glucose PET imaging, doses absorbed during germanium-based transmission scans were almost negligible. On the other hand, absorbed doses from CT-based transmission scans were significantly higher, particularly with a whole-body scanning protocol. Effective doses were 8.81 mSv in the high-speed mode and 18.97 mSv in the high-quality mode for whole-body CT-based transmission scans. These measurements revealed that the doses received by a patient during CT-based transmission scanning are more than those received in a typical PET examination. Therefore, the radiation doses represent a limitation to the generalised use of CT-based transmission measurements with current PET/CT scanner systems.