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Abstract Background A recent qualitative study in Denmark showed that genital warts (GWs) can considerably lower the quality of life of heterosexual patients. In this follow-up study, we interviewed men having sex with men (MSM) suffering from GWs to obtain an in-depth understanding of their perception of GWs and determine the extent to which minority (homosexual) cultural issues affect these patients' experiences. Qualitative interviews with six MSM were performed using a semi-structured interview guide. Questions were formulated on the basis of the earlier qualitative study in heterosexual patients with GWs along with a literature review. Data were analysed using a medical anthropological approach. Findings Many MSM worried about being stigmatised and excluded from the small homosexual 'scene', their key social group, thereby lowering their chances of finding sex and love. Most participants had suffered from GWs for several years which added to the negative psycho-sexual and social effects of the disease. Participants' fears of developing anal cancer were similar to those expressed about cervical cancer by females with GWs. Conclusions Ano-genital human papillomavirus (HPV) infection is common and has a serious psychological and sexual impact among MSM. However, they do not benefit to the same extent as heterosexual men from the herd immunity effect of HPV vaccination of girls. The pathological profile and concerns specific to MSM should be addressed when communicating with these patients, and should be taken into account when considering HPV vaccination of boys.