Objectives The aim of this study was to conduct a nationwide high-risk human papillomavirus (HR-HPV) infection genotyping analysis of women attending gynecological clinics. In addition, this study aimed to identify factors that are associated with HR-HPV infection. Methods This was a cross-sectional survey-based study with 759 participants. Demographics, lifestyle, and medical history data was collected with a questionnaire that was filled by gynecologists during patients’ visit. Cervical swabs were used as a source for HPV genotyping using AmpliSens kit. Data analysis was carried out which included descriptive statistics consisting of mean values, standard deviations, and frequencies, where applicable. To identify factors associated with HPV infection status, ordinal logistic regression was built. Results The mean age of the participants was 36.51 ± 10.09 years. The majority of women who participated in this study were aged between 26 and 35 years. Less than half of the women (39%) were HPV positive, 26% of participants had a single HR-HPV and 13% had multiple HR-HPV infections. The most prevalent HR-HPV genotypes were HPV-16 (54%), HPV-51 (7%), HPV-68 (7%), and HPV-18 (6%). The results of ordinal logistic regression demonstrated that factors such as older age, not being single, and having history of sexually transmitted infections (STIs), decrease the odds of having HPV infection. Conclusion This study identified high prevalence of HR-HPV among Kazakhstani women. Apart from this, our results showed that adding HPV testing to compulsory cervical cancer screening in Kazakhstan could help to improve the screening program and decrease the rates of cervical cancer.