We collected rare cases of recurrent respiratory papillomatosis (RRP) undergoing malignant transformation. We sought to identify human papillomavirus (HPV) subtypes in areas of papilloma, dysplasia, and carcinoma and investigate the pattern of protein overexpression. Three patients whose disease underwent malignant transformation from RRP to carcinoma were subjected to this study. Morphologically distinct areas in the pathology specimen of each patient were diagnosed as papilloma, dysplasia, and carcinoma. Each lesion was separately obtained by laser capture microdissection and was PCR amplified for the presence of HPV. A DNA chip was used to determine the type of HPV in each area. Immunohistochemistry for p53, Ki-67, and pRb was performed. HPV type 6 was present in all specimens tested positive. Expression of p53 and Ki-67 increased with increasing severity of dysplastic change. Although HPV type 11 is most frequently associated with malignant change of RRP, HPV type 6 may also contribute to play an equally important role in RRP carcinogenesis.