The pathologic diagnosis of various thyroid lesions can be challenging in the everyday practice of pathology. The two lesions that comprise a major portion of difficult cases in thyroid pathology include the follicular variant of papillary thyroid carcinoma and papillary carcinoma arising in association with lymphocytic thyroiditis. Both these neoplasms are equally difficult to diagnose from cytology and surgical pathology specimens. This article will provide a broad review of pathologic diagnosis, differential diagnosis, and the role of special studies in the diagnosis of these lesions. In addition, a practical approach to the pathologic diagnosis of these lesions is given on the basis of recent literature and personal experiences.