Papillary immature metaplasia (PIM) is a variant of human papillomavirus (HPV) 6 or 11 infection. PIM resembles an immature metaplasia but has filiform papillae, variable cytological atypia, and, frequently, extension into the endocervical canal. Because the unusual morphology and presentation of PIM may cause confusion between this and other benign and malignant papillary neoplasms, we conducted a clinicopathologic analysis of PIM and compared expression of Ki-67 between PIM, condyloma, and papillary carcinoma. Data on patient age, duration of the lesions, and procedures, including cone biopsy, were obtained. The distribution and intensity of staining for Ki-67 in the epithelium was recorded and compared with both condyloma and papillary carcinoma. HPV typing was performed by polymerase chain reaction (PCR) and restriction fragment length pleomorphism analysis (RFLP). Ten of 13 PIMs were HPV 6/11 positive. Three cases contained areas closely resembling condyloma. Eleven cone biopsies were performed on nine cases. Three were found to have a coexisting high-grade squamous intraepithelial lesion that was either HPV 6/11 negative or contained another HPV type. All PIMs displayed variable staining for Ki-67 with a low index of staining in the mid and upper epithelial layers. In contrast, areas of condyloma had significantly stronger staining in areas with viral cytopathic effect (koilocytosis). Six papillary carcinomas were analyzed and displayed moderate to diffuse staining, including staining of the superficial cell nuclei. PIM is a distinct pathological subset of cervical condyloma that frequently is managed by cone biopsy and may persist. The marked reduction in Ki-67 staining in superficial cell layers distinguishes PIM from some condylomata and most HSILs and papillary carcinomas. Immunostaining thus may be helpful in distinguishing PIM from papillary carcinoma, although the differentiation of the two is best made on morphological grounds.