PurposeMultiple punctate echogenic foci (MPEF) on thyroid ultrasonography reflects psammoma bodies in papillary thyroid carcinomas. However, MPEF is also observed in benign thyroid lesions. The aim of this study was to determine the origin of MPEF in patients with benign thyroid lesions.MethodsWe enrolled 26 patients with Graves’ disease (GD) and 24 with follicular nodular disease (FND) who exhibited MPEF and underwent surgery. As controls, we enrolled 40 patients with GD and 32 with FND, but without MPEF, who underwent surgery.ResultsMPEF was observed in both lobes in 80.8% of GDs with MPEF, but was limited to a single lobe in the remaining cases. MPEF was diffusely distributed in 72.3% of the cases and focally distributed in the remaining cases. On ultrasonography, most (92.3%) FNDs with MPEF were solid lesions, and seven nodules (26.9%) were interpreted as intermediate suspicion and their frequencies were higher than in those without MPEF (p < 0.01). Microscopically, calcium oxalate (CaOx) crystals were observed more frequently in GDs and FNDs with MPEF (100% and 88.5%, respectively) than in those without MPEF (p < 0.001). These differences were particularly significant for CaOx crystals > 100 μm. In GD cases, large CaOx crystals were observed more frequently in the lobes with MPEF than in those without (p < 0.05). No psammoma bodies were present in any of the cases.ConclusionAppearance of MPEF in GDs and FNDs is not because of psammoma bodies; it is attributable to CaOx crystals larger than 100 μm. Therefore, MPEF is not an indicator of malignancy.