OBJECTIVE. The objective of this study was to determine the optimal breathing protocol for combined PET/CT scans of the thorax. SUBJECTS AND METHODS. Eighty combined PET/CT scans were obtained in 64 patients (30 women, 34 men; mean age, 57 years; range, 19-86 years). The 80 PET/CT scans consisted of five group of patients (16 PET/CT scans per group) who underwent whole-body combined F-18-FDG PET/CT with different CT breathing protocols: expiration, mid suspended breath-hold, quiet breathing, small breath in, and regular breath in. The quality of alignment was analyzed at the diaphragm, aortic arch, heart, thoracic spine, and lung apices using a scale of ratings from I (very poor) to 5 (excellent). The Kruskal-Wallis test was used to compare alignment between breathing protocols for each anatomic reference point. RESULTS. Alignment of the PET and CT data sets was excellent with three breathing protocols: expiration, mid suspended breath-hold, and quiet breathing, with no statistical differences. Significant misalignment occurred at the diaphragm (p < 0.0001) and heart (p < 0.0001) with the small breath-in and regular breath-in techniques. CONCLUSION. Excellent image fusion of combined PET/CT data sets in the thorax, especially at the diaphragm and heart, can be achieved with expiration, mid suspended breathhold, or quiet breathing. Quiet breathing is recommended for optimal patient comfort during acquisition of attenuation-correction CT data sets.