It is difficult to distinguish benign from malignant follicular thyroid tumors by histological or cytological examination. The goal of this study was to reveal gene expression variations between benign and malignant follicular lesions of the thyroid gland. We investigated gene expression profiles from 24 follicular thyroid tumors (12 carcinomas and 12 adenomas) and 13 normal thyroid tissues using high-density human cDNA arrays. The identification of gene expression changes was based on signal intensity ratios of tumor versus normal thyroid parenchyma. Expression patterns of a set of known genes were found to be significantly different between follicular adenomas and follicular carcinomas. Our results demonstrate a potential use of gene expression profiling for differentiating benign from malignant follicular thyroid tumors. A detailed investigation of the differentially expressed genes could give new insights into molecular pathways of malignant transformation of thyroid follicular neoplasm and may help to develop a molecular tool for the preoperative differential diagnosis.