We aimed to investigate whether patients with genital warts experience greater feelings of shame and lower self-esteem compared with controls. Sixty patients with genital warts were compared with 60 asymptomatic genitourinary (GU) medicine patients and 60 orthopaedic outpatients. The shame scores of those with warts (31.08) were significantly higher (P < 0.0001) than either control group (GU medicine controls 20.77; orthopaedic controls 19.00). The impact on health-related quality of life (HRQoL) by each of the individual emotional parameters of shame, low self-esteem, intrusive thoughts, avoidance behaviour and self-efficacy impact was examined in the wart sample group. Only internalized shame (P = 0.001) and intrusive thoughts (P < 0.0001) were significant in predicting HRQoL scores. There are emotional implications in having genital warts, which can have a profound effect on a patient's quality of life and these need addressing just as much as the physical warts.