The introduction of combined PET/CT systems has a number of advantages, including the utilisation of CT images for PET attenuation correction (AC). The potential advantage compared with existing methodology is less noisy transmission maps within shorter times of acquisition. The objective of our investigation was to assess the accuracy of CT attenuation correction (CTAC) and to study resulting bias and signal to noise ratio (SNR) in image-derived semi-quantitative uptake indices. A combined PET/CT system (GE Discovery LS) was used. Different size phantoms containing variable density components were used to assess the inherent accuracy of a bilinear transformation in the conversion of CT images to 511 keV attenuation maps. This was followed by a phantom study simulating tumour imaging conditions, with a tumour to background ratio of 5:1. An additional variable was the inclusion of contrast agent at different concentration levels. A CT scan was carried out followed by 5 min emission with 1-h and 3-min transmission frames. Clinical data were acquired in 50 patients, who had a CT scan under normal breathing conditions (CTAC(nb)) or under breath-hold with inspiration (CTAC(insp)) or expiration (CTAC(exp)), followed by a PET scan of 5 and 3 min per bed position for the emission and transmission scans respectively. Phantom and patient studies were reconstructed using segmented AC (SAC) and CTAC. In addition, measured AC (MAC) was performed for the phantom study using the 1-h transmission frame. Comparing the attenuation coefficients obtained using the CT- and the rod source-based attenuation maps, differences of 3% and <6% were recorded before and after segmentation of the measured transmission maps. Differences of up to 6% and 8% were found in the average count density (SUV(avg)) between the phantom images reconstructed with MAC and those reconstructed with CTAC and SAC respectively. In the case of CTAC, the difference increased up to 27% with the presence of contrast agent. The presence of metallic implants led to underestimation in the surrounding SUV(avg) and increasing non-uniformity in the proximity of the implant. The patient study revealed no statistically significant differences in the SUV(avg) between either CTAC(nb) or CTAC(exp) and SAC-reconstructed images. The larger differences were recorded in the lung. Both the phantom and the patient studies revealed an average increase of approximately 25% in the SNR for the CTAC-reconstructed emission images compared with the SAC-reconstructed images. In conclusion, CTAC(nb) or CTAC(exp) is a viable alternative to SAC for whole-body studies. With CTAC, careful consideration should be given to interpretation of images and use of SUVs in the presence of oral contrast and in the proximity of metallic implants.