The diagnostic problems arising from frozen section evaluation of thyroid lesions are complex and beclouded in controversy. Prime examples include follicular and Hurthle cell neoplasms, both of which lack standardization in classification and management. The seemingly straightforward identification of papillary carcinoma is often complicated by the frequent absence of its distinguishing features, some of which are reportedly restricted to formalin-fixed paraffin embedded material. Thyroiditides and thyroidal ectopias present unique and separate differential diagnostic considerations that at the time of frozen section may pose problems for surgeon and pathologist alike. These issues and their controversial aspects are addressed, and potential diagnostic pitfalls related to frozen section diagnosis of thyroid lesions in general are outlined. An analysis of 300 thyroid frozen sections over a 5-year period and the histologic frozen section features of 40 papillary thyroid carcinomas are also presented. The presence of optically clear nuclei was identified in frozen sections from 15 cases, and was extensive in one. Thirty-eight of 40 cases displayed optically clear nuclei within permanent sections. It is suggested that this cytologic feature is not the exclusive domain of permanent section, and when present in the frozen section may be helpful in identifying papillary carcinoma, especially when an obvious papillary component is lacking.