The fusion of computed tomography (CT) and positron emission tomography (PET) may improve diagnostic accuracy, but is limited by different breathing protocols. This study aimed at quantifying respiration-induced alignment errors. PET-CT was acquired in 24 patients. Contrast-enhanced whole-body CT was obtained in a single breath hold in the expiratory state of a normal breathing cycle. An inspiratory low-dose CT of the thorax was acquired in the same session, and comparison of the two CT scans was used to assess the potential mismatch of PET and CT fusion. The largest craniocaudal expansion was found in the area of the diaphragm. A considerable sagittal expansion was found in the anterior parts of the lungs. Central tracheo-bronchial structures were displaced during inspiration mainly in the anterior and caudal directions. The craniocaudal shift of central structures showed a linear correlation with the diaphragmatic expansion, whereas the sagittal shift correlated with the sagittal pleural expansion. There was, however, no correlation between craniocaudal and sagittal respiratory motion. Alignment errors are most severe in the base of the lung, but central structures are affected, too. Understanding of the main vectors of respiratory motion may help in image interpretation when PET and CT are acquired separately.