The relation between the detection of clue cells in cervical smears of women with CIN and the expression of COX-2 in these lesions were determined. Samples from 228 women, treated due to CIN and who underwent cervical conization, were obtained. Hybrid Capture II and Pap smear samples were collected immediately before performing conization. Pathological diagnoses were 11 (5%) normal cervix, 35 (15%) CIN1, 31 (14%) CIN2, and 151 (66%) CIN3. COX-2 immunoreactivity grading on the pathological specimens was based on the German ImmunoReactive score. In cervical smears, 20 fields (40x) were examined, each of them with a minimum count of 10 epithelial cells. When 20% or more of clue cells were detected the sample was considered positive for clue cells. The prevalence of clue cells was similar across histological strata (P = 0.42). Although the expression of COX-2 did not differ in lesions with varying severities (P = 0.24), there was a negative association between the expression of COX-2 and the presence of clue cells in Pap smear (OR = 0.4; 95% CI = 0.2-0.9): only 12% of women with moderate and strong expression of COX-2 had clue cells in their smears, contrasted to 22% of those with negative and weak expression of COX-2. HPV infection was associated in a borderline manner to the expression of COX-2 (P = 0.04; OR = 2.3 95% CI = 1.0-5.4). The reduced expression of COX-2 in CIN specimens may suggest that clue cells interfere with the inflammatory component of the carcinogenic process that lead to CIN.