Thyroid neoplasms represent a broad spectrum of tumors with different biologic behaviors. The majority of these tumors can be readily diagnosed by characteristic histopathologic features, but the distinction between follicular adenomas and follicular carcinomas can be difficult. Recent studies with cell cycle proteins such as p27kip1 (p27), a cell cycle inhibitory protein, and Ki-67, a proliferation marker, suggest that these markers might be useful in predicting the behavior of various neoplasms. We analyzed 95 thyroid lesions (16 follicular adenomas, 23 follicular carcinomas, 22 papillary carcinomas, 27 anaplastic carcinomas, plus 7 non-neoplastic thyroids [NNTs], used as a control group) for expression of p27 and Ki-67 by immunostaining. The distribution of immunoreactivity was analyzed by quantifying nuclear staining in each case without knowledge of the diagnosis or outcome. Clinical history and follow-up information were obtained by chart review. There were significant differences in the expression of p27 between follicular adenomas (labeling index [LI] = 47.9+/-5.6) and follicular carcinomas (LI = 15.7+/-2.0). Papillary carcinomas (LI = 11.6+/-3.0) and anaplastic carcinomas (LI = 9.4+/-1.7) had p27 LIs similar to that of follicular carcinomas; the NNT group had the highest p27 LI (74.1+/-4.9). The Ki-67 LI of anaplastic carcinomas (57.6+/-3.8) was more than threefold greater than that of any other group. Logistic regression showed that p27 was effective in distinguishing follicular adenomas from follicular carcinomas (P = .0056) and that Ki-67 could also distinguish follicular adenomas from follicular carcinomas (P = .0060). Analysis of follicular carcinomas with and without metastases showed significantly higher expression of Ki-67 in patients with metastases (P = .0019). These results indicate that antibodies to p27 and Ki-67 might be useful in distinguishing between thyroid neoplasms that are difficult to diagnose by the usual histopathologic criteria.