Objectives To assess the prevalence and correlates of self-reported genital warts (GWs) among women and men aged 18–45 years in the Baltic countries.

Methods In 2011–2013 we performed a cross-sectional survey using a self-administered questionnaire to collect information on the history of clinically diagnosed GWs, sociodemographic characteristics and sexual behaviour. Probability sampling methods were used to invite 16 959 individuals representing the general population, of whom 7760 (45.8%) participated (Estonia: 1967 women, 1221 men; Latvia: 1525 women, 1525 men; Lithuania: 1522 women).

Results The estimated lifetime prevalence of clinically diagnosed GWs in women was 4.6% (95% CI 3.8 to 5.5) in Estonia, 2.9% (95% CI 2.0 to 3.6) in Latvia and 1.5% (95% CI 1.2 to 2.0) in Lithuania. Among men, the corresponding values were 2.8% (95% CI 1.9 to 4.0) in Estonia and 1.9% (95% CI 1.3 to 2.6) in Latvia. The mean age at first episode of clinically diagnosed GW was 24.6 years (95% CI 23.6 to 25.5) for women and 24.5 years (95% CI 22.9 to 26.0) for men. A lifetime history of clinically diagnosed GW was associated with a history of sexually transmitted infections other than GW (adjusted OR (AOR) 3.0, 95% CI 2.1 to 4.3 for women; AOR 5.3, 95% CI 3.0 to 9.2 for men), and a higher number (5+) of lifetime sexual partners (AOR 2.9, 95% CI 1.9 to 4.2 for women; AOR 2.1, 95% CI 1.2 to 3.9 for men). Men living comfortably within their household income had higher odds for GW (AOR 1.9, 95% CI 1.1 to 3.2).

Conclusions Our estimated prevalence of clinically diagnosed GWs was lower than estimates from the general population of other European countries.