The aim of this study was to evaluate wether HBME-1 immunohistochemical analysis can reliably differentiate benign thyroid lesions from thyroid carcinomas. Fifty benign and 87 malignant lesions were analyzed. All papillary carcinomas (67/67) were HBME-1 positive, as well as 14 of 20 follicular well-differentiated carcinomas and 13 of 29 atypical follicular adenomas and 4 out of 21 goiters were weakly and focally positive. HBME-1 highlighted micronests of papillary carcinomas. The reactivity of HBME-1 in the tall-cell variant of papillary carcinomas was apical and stronger than in classical papillary carcinomas. Positive HBME-1 immunostaining is in support of the diagnosis of the follicular variant of papillary carcinoma and highlights micropapillary carcinomas. HBME-1 may be of additional value in the diagnosis of thyroid malignancy.