Background Vaccination against the human papillomavirus (HPV) has the potential to significantly reduce morbidity and mortality associated with genital warts and HPV-related cancers. However, HPV vaccination rates continue to be suboptimal among the “catch-up” population of 18- to 26-year-old women. One consistent risk factor for nonvaccination is being in a relationship. This study aimed to understand how relationship status and vaccination status impact risk perceptions and perceived need for the HPV vaccine among young adult women. Methods In-depth interviews were conducted with a sample (n = 50) of recently HPV vaccinated and unvaccinated college women, and stratified by four relationship categories. Comparative thematic analysis was used to assess relationship status and HPV risk perceptions. Results Women in relationships perceived their risk of HPV to be low, which they attributed to monogamy and few sexual partners. Women in dating relationships reported higher HPV risk, which was linked to unprotected sex and sexual activity. In contrast, single women stated that their low risk for HPV was due to sexual inactivity. Conclusions This study builds on the epidemiological literature, by understanding how relationship status impacts HPV vaccination among young adult women. Relationship status contributed to HPV risk perceptions and vaccination decisions among these women. Perceptions were framed based on sexual behavior, such as monogamy or number of sexual partners. Future efforts should tailor health messages to young adult women's specific risk misperceptions about HPV.