Image misregistration can occur in fusion PET/CT, because of motion artifacts caused by the management of respiration. The standard imaging protocol of the CT component of PET/CT is normal expiration (NormExp) or free breathing (FB). The objective of this study was to compare NormExp and FB for the optimal breathing protocol for PET/CT scans. A total of 600 consecutive patients were examined using lutetium oxyorthosilicate (LSO)-based PET/CT. CT was acquired during NormExp (i.e., the level reached when the patient exhaled without forcing expiration and then held the breath) in 300 patients and during FB in 300 patients. The profile of liver measured along body axis was assessed. The distance of profile centers between the PET image and the CT image was measured. The misalignment between profile centers (PET) and profile centers (CT) was compared between NormExp and FB using the histogram of patients. An F test was used to test if the variances of two misalignments are equal. Next, the relationship between misalignment and age was evaluated in two managements of respiration. There was no significant difference between NormExp and FB in the histogram. However, significant misalignments (>10 cm) were found with NormExp. Patient age may have influenced the mismatch. FB is recommended for geriatric patients during acquisition of attenuation correction CT data sets.