The aim of this study was to evaluate the correlation between clinical behavior and expression of human papillomavirus (HPV) in patients with juvenile laryngeal papillomatosis, in an attempt to develop an effective molecular biological method to predict prognosis. We included 37 patients with juvenile laryngeal papillomatosis in the study group and 10 cases each of juvenile vocal cord polyps and juvenile normal laryngeal mucosa as the control group. We detected HPV by immunocytochemistry and in situ hybridization, identified the virus type, and measured HPV-DNA content using a computer-assisted, color pathological image-analysis system. Additionally, we conducted a retrospective study with regard to the patients' clinical history to evaluate the prognosis. The data of the 2 groups were compared and statistically analyzed, including a correlation with prognosis. In the study group, 67.3% (25/37) were positive for HPV-Ag by immunocytochemistry; whereas 53.2%, 45.8%, and 25.4% were positive for HPV6b-DNA, HPV11-DNA, and HPV6b+11-DNA, respectively, by in situ hybridization. HPV was not detected in the control group. There was a significant difference between two groups (P < 0.05). Compared to HPV11-DNA-positive cases, those that were positive for HPV6b-DNA and HPV6b+ 11-DNA showed lower results on average, for age at first diagnosis and self-relief, number of surgeries, and interval between surgeries. Our findings suggest that immunocytochemistry and in situ hybridization are useful methods to evaluate the prognosis of juvenile laryngeal papilloma (JLP) and that HPV6b-positivity can be used as an index to predict the development and outcome of JLP.