Background: There is a growing need for a reproducible and effective imaging method for the quantitative differentiation of benign from malignant thyroid nodules. This study aimed to investigate the performances of intravoxel incoherent motion (IVIM) parameters and the apparent diffusion coefficient (ADC) in differentiating malignant from benign thyroid nodules derived from the most repeatable region of interest (ROI) delineation. Methods: Forty-three patients with 46 pathologically confirmed thyroid nodules underwent diffusion-weighted imaging (DWI) with 8 b values. Two observers measured the intravoxel incoherent motion (IVIM) parameters (D, f and D*) and the apparent diffusion coefficient (ADC), ADC 600 and ADC 990 values using whole-lesion (W-L) ROI and IVIM parameters using single-section (S-S) ROI delineation. The intraclass correlation coefficients (ICCs) and Bland-Altman plots were used to evaluate the intra-and interobserver variability. The diagnostic performance of these parameters was evaluated by generating receiver operating characteristic (ROC) curves. Results: The ICC values of all IVIM with W-L ROI delineation were higher than those with S-S ROI delineation, and excellent intra-and interobserver reproducibility was obtained. According to the Bland-Altman plots, the 95% limits of agreement of the IVIM parameters determined by the W-L ROIs revealed smaller absolute intra-and interobserver variability than those determined by S-S ROIs. The D and ADC 600 values obtained from the W-L ROIs were the most powerful parameters in differentiating benign from the malignant nodules [area under the ROC curve = 0.962 and 0.970, P = 0.771]. Conclusions: The W-L ROI of the thyroid was considered an effective method for obtaining IVIM measurements with excellent reproducibility for differentiating benign from malignant nodules.