Aim: To investigate clinical factors, especially pathogenic in the lower genital tract associated with cervical intraepithelial neoplasia (CIN) among women participating in a cervical cancer (CC) screening program in Liuzhou, south of China. Materials and Methods: A hospital-base case-control study for four years was designed. A total of 12,644 outpatients were involved in this study. Clinical characters were recorded and samples of the cervical secretion were obtained to detect Chlamydia trachomatis (CT), high-risk human papillomavirus (HR-HPV), low-risk HPV (LR-HPV), Neisseria gonorrhoeae (NG), and Ureaplasma urealyticum (UU). Logistic regression models were conducted to investigate the association between the factors and CIN. Results: There were 260 CIN patients of all included cases (2.06%). HR-HPV (OR=18.27, 95%CI 13.89-24.04), CT infection (OR=2.31 95%CI 1.70-3.13), numbers of pregnancy (OR=1.42, 95%CI 1.11-1.83), and older age (OR=1.59, 95%CI 1.16-2.19) were associated with CIN. The prevalence of CIN in patient group HR-HPV(+), CT(+), HR-HPV(+), CT(-); HR-HPV(-), CT(+); HR-HPV(-), and CT(-) was 18.00%, 10.26%, 1.97%, and 0.48%, respectively. Women both HR-HPV and CT positive had a significantly higher susceptibility to CIN (p < 0.001). Conclusion: Age and gravity might be risk factors of CIN. HR-HPV and CT play important roles in cervical carcinogenesis. Co-infection of HR-HPV, and CT might increase the risk of CIN.