In previous fluorine-18-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) studies, tumor segmentation using peritumoral halo layer (PHL; SegPHL) was shown to be reliable and accurate segmentation method in various malignant tumors. We found that the halo layer also was observed on the 99mTc-pertechnetate (99mTcO4) thyroid single photon emission computed tomography (SPECT)/CT. In the present study, we attempted to apply thyroid segmentation using the perithyroidal halo layer (PTHL; SegPTHL) on 99mTcO4 thyroid SPECT/CT and compared SegPTHL with CT-based thyroid segmentation (SegCT). A total of 33 patients (19 females, 14 males; mean age, 46.91±15.7 years old) were enrolled in this study. For SegCT, three-dimensional volume of interest (VOI) of the thyroid was generated via multiple 2-dimensional regions of interest (ROI) along the thyroid margin on transaxial CT images that were manually drawn slice by slice. The PTHL was easily identified by an abrupt increase in layer thickness with minimal or mild distortion of the main thyroid contour, and the thyroid margin for SegPTHL was determined at the innermost portion of PTHL. An automated VOI generation for SegPTHL was performed using the Q. Volumetrix software. The correlation and reliability tests were performed between the quantification parameters of SegPTHL and SegCT. The PTHL threshold adjusted according to maximal SUV of thyroid were similar to the results of previous SegPHLstudies of 18F-FDG PET/CT. A good correlation was observed between the thyroid volumes of SegCT and SegPTHL (r=0.725; P<0.0001), although the thyroid volume of SegPTHL was slightly larger than that of SegCT (P=0.0017). The % thyroid uptake (TcTU), total lesion activity (TLA), and mean standardized uptake value (SUVmean) of SegPTHL correlated well with those of SegCT (r=0.9877, 0.9883, 0.9875, respectively; P<0.0001). No significant error was observed between the parameters (i.e., TcTU, TLA, and SUVmean) of SegPTHL and SegCT. Thyroid segmentation PTHL may be a useful method for reliable quantification of thyroid uptake, because the SPECT/CT parameters of SegPTHL were strongly correlated with those of SegCT, as well as the process of SegPTHL is easier and faster than that of SegCT.