BACKGROUND Cervical cancer is the leading cause of cancer morbidity and mortality among women in Nepal and Bhutan. Data on high-risk human papillomavirus (HR-HPV) infection and cervical abnormalities among Nepali and Bhutanese women are sparse. The objectives of this study were to assess and compare the prevalence of HR-HPV infection and cervical abnormalities among Nepali and Bhutanese women living in Jhapa District in eastern Nepal; and examine the risk factors for HR-HPV infection and cervical abnormalities in those women. METHODS Study participants were recruited from a women's health camp organized by NFCC-International, a Nepal-based non-governmental organization, in 2014. Consenting participants were administered a demographic and health questionnaire and cervico-vaginal specimens collected. Both self-collected and clinician-collected cervico-vaginal specimens were tested for HR-HPV infection. Cytologic exam was performed on clinician-collected samples and cervical cytology results were categorized according to the Bethesda classification. A participant was classified as a Bhutanese if they were either born in Bhutan or currently lived in one of the United Nations administered Bhutanese refugee camps in Jhapa; otherwise, the participant was classified as a Nepali. RESULTS Of the 647 study participants, 15.9% were Bhutanese women living in refugee camps and the overall age (± standard deviation) was 38.8 ± 8.2 years. The prevalence of HR-HPV infection was 8.9% and abnormal cervical cytology was 7.1% respectively, with no significant difference in HR-HPV positivity (p = 0.399) or abnormal cervical cytology (p = 0.698) between Nepali and Bhutanese women. Compared to women whose husbands had not migrated for employment, women whose husbands had migrated outside of the district had 3.30 times (95% Confidence Interval [CI]: 1.13-9.64) the odds of being HR-HPV positive and women whose husbands had migrated outside the country had 2.92 times (95% CI: 1.32-6.49) the odds of having abnormal cervical cytology. CONCLUSIONS HR-HPV positivity and abnormal cervical cytology were similar among Nepali and Bhutanese women. Husbands migrating for employment within or outside the country was a significant risk factor for high-risk HPV infection and cervical cytology, indicating the important role spousal behavior may play in HR-HPV acquisition and cervical abnormalities among these women.