Average CT (ACT) and PET have a similar temporal resolution and it has been shown to improve registration of the CT and PET data for PET/CT imaging of the thorax. The purpose of this study was to quantify the effect of ACT attenuation correction on PET for gross tumor volume (GTV) delineation with standardized uptake value (SUV) for liver and esophageal lesions. Our study included 48 colorectal cancer patients with metastasis in the liver and 52 esophageal cancer patients. These patients underwent a routine PET/CT scan followed by a cine CT scan of the thoracic region for ACT. Differences between the two PET data sets (PET HCT and PET ACT ) corrected with the helical CT (HCT) and ACT were quantified by analyzing image alignment, maximum SUV (SUV max ), and GTV. The 67% of the colorectal and 73% of the esophageal studies demonstrated misregistration between the PET HCT and HCT data. ACT was effective in removing misregistration artifacts in 65% of the misregisted colorectal and in 76% of the misregisted esophageal cancer patients. Misregistration between the CT and PET data affected GTVs due to the change in SUV max with ACT. A change of SUV max greater than 20% between PET HCT and PET ACT was found in 15% of the colorectal and 17% of the esophageal cases. Our results demonstrated a more pronounced effect of misregistration for the smaller lesions (< 5 cm 3 ) near the diaphragm (< 5 cm). ACT was effective in improving registration between the CT and PET data in PET/CT for the colorectal and esophageal cancer patients.