The purpose of this study was to determine the existence, and viral load of human papilloma virus (HPV) subtypes 16 and 18 in paraffinized cervical intraepithelial neoplasia (CIN) samples by real-time polymerase chain reaction (RT-PCR). Overall 94 women were included. Of these patients 47 (50%) had CIN I, 27 (28.8%) had CIN II, and 20 (21.2%) had CIN III. HPV positivity for these three groups were 4.2%, 14.8% and 45%, respectively. HPV positivity in CIN III patients was significantly higher than CIN I (OR = 18.41, 95% CI 3.00-145.73; p < 0.001), and CIN II patients (OR = 4.70, 95% CI 1.00-23.76; p = 0.05). The difference between CIN I and II was not significant (p = 0.18). Viral loads were 10(2), and 10(4) copy/ml for two CIN I patients; 10(2), 10(3), and 10(5) for three CIN II patients; and 10(2), 10(3), 10(4), 10(4), 10(5), 10(5), and 10(6) copy/ml for eight patients with CIN III. Viral load of the remaining one patient could not be assessed. No significant variance was noted among the groups with respect to viral load (p = 0.73). RT-PCR had important advantages of detecting, typing, and quantifying at the same time. Although HPV positivity was increased significantly by the degree of lesions, this relation was not observed for viral load.