BACKGROUND: Increased extracellular matrix 1 (ECM1) expression, as determined by real-time reverse transcriptase-polymerase chain reaction (RT-PCR), has been recently proposed as a novel and independent diagnostic marker for malignant thyroid nodules. However ECM1 protein expression has not been previously evaluated in thyroid tumors. Real-time RT-PCR is not widely available and this has important implications for the widespread use of the expression of this gene for diagnosis. The purpose of the current study is to evaluate and compare ECM1 expression by real-time RT-PCR with immunohistochemistry (IHC) as diagnostic aids in thyroid neoplasms. MATERIALS AND METHODS: ECM1 expression was studied in normal thyroid tissues (n = 14) and primary thyroid tumors (19 benign, 30 malignant) using both techniques. The performance characteristics of ECM1 expression were examined with receiver operating characteristic curves and the resulting area under the curve. RESULTS: ECM1 was highly expressed in thyroid carcinomas, compared with benign thyroid tissues, both at the mRNA (P < 0.01) and protein (P = 0.06) levels. However, ECM1 mRNA expression appeared to be a more sensitive marker of thyroid malignancy than IHC (AUC = 0.77 and 0.65, respectively). ECM1 expression by both methods was useful in identifying malignant follicular, but not Hürthle cell neoplasms. CONCLUSIONS: We confirm that ECM1 expression has potential utility as an independent diagnostic marker for thyroid cancer, although, performance characteristics were lower than previously published. Furthermore, IHC was not as sensitive as real-time RT-PCR in identifying malignant lesions. Prospective studies are needed to further clarify the role of ECM1 expression as a diagnostic marker.