BACKGROUND: Screening for co-infections with HIV, HSV-2 and Chlamydia trachomatis (CT) among high-risk human papilloma virus (hr-HPV) positive women, coupled with enhanced counseling on contraceptives use remains essential in alleviating high morbidity of cervical cancer (CC). The aim of this study was to determine the prevalence of cervical intraepithelial neoplasia (CIN) among women referred for CC screening at a referral hospital in Kisumu County, Kenya; and to establish the role of co-infection and hormonal contraceptives on CIN. METHOD: In a cross-sectional study, we collected HPV, HIV, HSV-2 and CT data, cervical cytology results, and demographic information from 517 referrals. Blood samples were obtained for HIV and HSV-2 tests; urine for CT test, cervical swabs for hr-HPV test and colposcopic biopsy for histology confirmation after visual inspection with acetic acid (VIA). RESULTS: The overall prevalence of CIN was 18.4% (95/517) with CIN1 observed in 56(29.6%), CIN2 in 27(`14.3%), CIN3 and above (CIN3+) in 12(6.3%) and normal biopsy in 94(49.7%) of the patients out of which high grade CIN2 and above (CIN2+) was 7.54% (39/517) equivalent to 32.5 per 100,000 women per year. In a univariate analysis; HPV/HIV co-infection (infected vs. uninfected: OR 2.79; 95% CI 1.56-5.10, p < 0.001); HPV/HSV-2 co-infection (infected vs. uninfected: OR 2.41; 95% CI: 1.12-5.46, p < 0.024); HPV/CT co-infection (infected vs. uninfected: OR 3.83; 95% CI 1.84-8.51, p < 0.001) were found to be significantly associated with CIN. Additionally, hormone-containing intra uterine device (HIUD) contraceptives (users vs. none users: OR 1.43; 95% CI 0.28-10.9, p < 0.017) were also associated with CIN. CONCLUSION: Co-infections with HIV, HSV-2 or Chlamydia trachomatis and use of HIUD were associated with increased risk of testing positive for CIN in HPV positive women. Although the overall prevalence of CIN was high, high-grade CIN2 + was comparable to the rates reported earlier. Therefore, population screening for co-infections alongside hr-HPV is desirable and is likely to reduce the burden of CIN in the region. Besides, women positive for hr-HPV and opting for contraceptives ought to be counseled about the possible positive and negative side-effects of different contraception options.