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Background: Different cases exist in the measurement of thyroid radiobioassays owing to the individual characteristics of the subjects, especially the potential variation in the counting efficiency. An In situ Object Counting System (ISOCS) was developed to perform an efficiency calibration based on the Monte Carlo calculation, as an alternative to conventional calibration methods. The purpose of this study is to evaluate the applicability of ISOCS to thyroid radiobioassays by comparison with a conventional thyroid monitoring system. Materials and Methods: The efficiency calibration of a portable high-purity germanium (HPGe) detector was performed using ISOCS software. In contrast, the conventional efficiency calibration, which needed a radioactive material, was applied to a scintillator-based thyroid monitor. Four radioiodine samples that contained 125I and 131I in both aqueous solution and gel forms were measured to evaluate radioactivity in the thyroid. ANSI/HPS N13.30 performance criteria, which included the relative bias, relative precision, and root-mean-squared error, were applied to evaluate the performance of the measurement system. Results and Discussion: The portable HPGe detector could measure both radioiodines with ISOCS but the thyroid monitor could not measure 125I because of the limited energy resolution of the NaI(Tl) scintillator. The 131I results from both detectors agreed to within 5% with the certified results. Moreover, the 125I results from the portable HPGe detector agreed to within 10% with the certified results. All measurement results complied with the ANSI/HPS N13.30 performance criteria. Conclusion: The results of the intercomparison program indicated the feasibility of applying ISOCS software to direct thyroid radiobioassays. The portable HPGe detector with ISOCS software can provide the convenience of efficiency calibration and higher energy resolution for identifying photopeaks, compared with a conventional thyroid monitor with a NaI(Tl) scintillator. The application of ISOCS software in a radiation emergency can improve the response in terms of internal contamination monitoring.