Attenuation correction (AC) of PET images with helical CT (HCT) in PET/CT matches only the spatial resolution of CT and PET, not the temporal resolution. We therefore proposed the use of respiration-averaged CT (ACT) to match the temporal resolution of CT and PET and evaluated the improvement of tumor quantification in PET images of the thorax with ACT. First, we examined 100 consecutive clinical PET/CT studies for the frequency and magnitude of misalignment at the diaphragm position between the HCT and the PET data. Patients were injected with 555-740 MBq of (18)F-FDG and scanned 1 h after injection. The HCT data were acquired at the following settings: 120 kV, 300 mA, pitch of 1.35:1, collimation of 8 x 1.25 mm, and rotation cycle of 0.5 s. Patients were instructed to hold their breath at midexpiration during HCT of the thorax. The PET acquisition was 3 min per bed. Second, we retrospectively analyzed studies of 8 patients (1 with esophageal cancer and 7 with lung cancer). Each study included regular PET/CT followed by 4-dimensional (4D) CT for radiation treatment planning. We compared the results of AC of the PET data with HCT and ACT. There were 13 tumors in these 8 patients. The 4D CT data were acquired at the following settings: 120 kV, 50-150 mA, cine duration of 1 breathing cycle plus 1 s, collimation of 8 x 1.25 mm, and rotation cycle of 0.5 s. The acquisition was taken when the patient was in the free-breathing state. We averaged the 10 phases of the 4D CT data to obtain ACT for AC of the PET data. Both the ACT and the HCT data were used for AC of the same PET data. There was a misalignment between the HCT and the PET data in 50 of 100 patient studies. In 34 studies, the misalignment was greater than 2 cm. In a comparison of HCT and ACT, 5 tumors had differences in standardized uptake values (SUV) between HCT-and ACT-attenuation-corrected PET of less than 20%, and 4 tumors had differences in SUV of more than 50%. The latter 4 tumors were found in the patient with esophageal cancer and in 2 of the patients with lung cancer. The PET data from these 3 patients had a misalignment of 2-4.5 cm relative to the HCT data. Breathing artifacts were significantly reduced by ACT. Seven of the 8 patients had a lower diaphragm position on HCT than on ACT, suggesting that the patients tended to hold a deeper breath during HCT than during ACT. The high rate of misalignment suggested a potential mismatch between the HCT and the PET data with the limited-breath-hold CT protocol. In the comparison of HCT and ACT, significant differences (>50%) in SUV were attributable to different breathing states between HCT and PET. The PET data corrected by ACT did not show breathing artifacts, suggesting that ACT may be more accurate than HCT for AC of the PET data.