Human papillomavirus (HPV) 16 DNA can be integrated into the DNA of cells, thereby disrupting E2 gene expression, which leads to increased expression of the E6 and E7 viral oncogenes and progression to cancer. However, the relationships among HPV viral load, cytologic diagnosis, and HPV integration status remain unclear. The aim of this study was to evaluate the HPV type distribution, viral load, and HPV 16 integration status, and then investigate their relationships with precancerous and cancerous lesions among Japanese women of different age groups. Liquid-based cytology (LBC) samples were examined by quantitative real-time polymerase chain reaction (PCR). The overall mean prevalences of HPV were higher in younger women and lower in middle-aged women among the age groups. The positivity rate of HPV 16 peaked at a younger age than that of all HPV subtypes. The HPV 16 viral load per cell decreased from a low-grade squamous intraepithelial lesion (LSIL) to a cancerous lesion (257.4 for LSIL, 76.9 for high-grade squamous intraepithelial lesions, and 35.7 for cancerous lesions). The average HPV 16 DNA copy numbers for three different HPV 16 integration statuses were 64.1 for the episomal form, 465.5 for the mixed form, and 0.4 for the integrated form. Furthermore, the mean age of patients with the pure integrated form of HPV 16 was more than 10 years older than those of patients with the episomal and mixed forms. Quantitative real-time PCR appears to be a useful method for quantitative and physical status analyses of HPV in cervical cancer screening with LBC samples.