The aim of this study was to evaluate the respiration position, which is optimal for co-registration of abdominal CT images, and the corresponding positron emission tomography (PET) scan in a new combined PET/CT system. Ten patients (5 men, 5 women; age 57.7+/-15.3 years, age range 34-80 years) underwent imaging for tumor staging on a combined PET/CT scanner (Discovery LS, GE Medical Systems, Milwaukee, Wis.). The PET emission images were acquired during normal shallow breathing and during CT scanning the patients performed four different breathing tasks: free breathing (FB); maximum inspiration (MaxInsp); maximum expiration (MaxExp); and normal expiration (NormExp). NormExp was defined as the respiratory level that was reached when the patient first inhaled and then exhaled without forcing expiration, and then held the breath in this position. Movements of the spleen, liver, left and right kidney, and the bladder were measured by using the promontory of the sacrum as a reference point and measuring the distance from this point to the abdominal organs in the PET and CT images by two independent observers. Statistical comparison of the measured distances between the CT scans and the PET scan were made using a Wilcoxon signed-rank test with Bonferroni correction. Repeated-measures analysis of variance served for the assessment of intraobserver and interobserver agreement. There was no significant difference between NormExp and FB indicating that both respiration protocols are suitable for PET/CT image co-registration of abdominal studies. In contrast, the MaxExp and MaxInsp protocol are not suitable. The NormExp and FB respiration protocol are both suitable for the co-registration of abdominal PET/CT studies. In most patients the mismatch of abdominal organs will be lower than the resolution of the final co-registered PET/CT image.