The aim of this study was to determine the optimal acquisition scan protocol for deep inspiration breath-hold (BH) fluoro-2-deoxy-D-glucose positron emission tomography (PET) for the examination of thoracic lesions. We studied 32 thoracic lesions in 21 patients. Whole-body PET/computed tomography (CT) scanning with free breathing (FB) was performed for 3 min per bed position, followed by a BH-CT and five BH-PET for 20 s each. Summed BH images with total acquisition times of 40, 60, 80 and 100 s were generated (BH × 2, BH × 3, BH × 4 and BH × 5, respectively). The displacements between PET and CT images, the lesion volume of the PET image, the maximum standardized uptake value (SUVmax) and the quality of the PET image were assessed in relation to the clinical characteristics of each patient and the summation of the BH-PET images. BH-PET decreased the tumor volume significantly (FB: 7.23 ± 9.70 cm³, BH × 5: 4.71 ± 5.14 cm³, P<0.01) and increased the SUVmax (FB: 6.27 ± 5.41, BH × 5: 7.53 ± 6.28, P<0.01). The displacement between the PET and CT images was improved significantly in the BH scans (FB: 0.77 ± 0.53 cm, BH × 5: 0.36 ± 0.24 cm, P<0.01). In addition, aging and lung function of patients influenced the reproducibility of BH-PET. The summed BH-PET images, obtained by summation of three or more BH-PET images (total acquisition time of 60 s or more), achieved good image quality. BH-PET/CT improved the misregistration between PET and CT images and increased the SUVmax of thoracic lesions. The recommended number of BH-PET images for summation with 20 s of acquisition time is three or more.