In patients, who undergo surgery for hyperthyroidism, many cases of incidental thyroid cancer (ITC) have been detected. In the literature, there is no study about ITC in subcentimeter nodules in these patients. We performed this study to determine the frequency of ITC in subcentimeter nodules and ultrasonographic features that can predict malignancy in the patients with hyperthyroidism. We retrospectively reviewed our database about 3114 patients, who underwent thyroidectomy in our hospital. Among 869 patients (27.9%), who were operated because of hyperthyroidism, we enrolled 337 patients, who underwent total thyroidectomy and had subcentimeter nodule [59 Graves’ disease (GD) 98 subcentimeter nodule; 278 toxic multinodular goitre (TMNG), 359 subcentimeter nodule], in this study. Twenty-five nodules with ITC and 432 benign nodules have been detected and compared for ultrasonographic (US) features. Incidental thyroid cancer detection ratio was 5.4% [10.2% (10/98) in subcentimeter thyroid nodules in individuals with GD, and 4.1% (15/359) in individuals with TMNG, P = 0.018)]. Significant differences have been observed between the groups in terms of microcalcification in US examination of malign and benign subcentimeter thyroid nodules and the ratio of anterioposterior diameter to transverse diameter (A/T) ≥1 [(OR = 5.172; 95% CI: 1.495–17.886, P = 0.015), and (OR = 5.930; 95% CI: 1.531–22.971, P = 0.007), respectively]. We detected a higher incidence of ITC in subcentimeter thyroid nodules in GD compared to TMNG. US examination of subcentimeter nodules in hyperthyroid individuals has indicated that microcalcification and ratio of A/T ≥1 are the parameters that predict malignancy.