Kyrgyzstan reported 77.5 new human brucellosis cases per 100,000 people in 2007, which is one of the highest incidences worldwide. In Kyrgyzstan, the currently used diagnostic tests in humans and animals are the Rose Bengal Test and the Huddleson test. A national representative cross-sectional study using cluster sampling proportional to size in humans, cattle, sheep, and goats was undertaken to assess the apparent seroprevalence in humans and animals. A total of 4,936 livestock sera and 1,774 human sera were tested in Naryn, Chuy, and Osh Oblasts. The overall apparent seroprevalences of brucellosis were 8.8% in humans (95% CI 4.5-16.5), 2.8% (95% CI 1.6-4.9%) in cattle, 3.3% (95% CI 1.5-6.9%) in sheep, and 2.5% (95% CI 1.4-4.5%) in goats. Naryn Oblast had the highest seroprevalences in humans and sheep. More men than women were seropositive (OR = 1.96; P < 0.001). Human seroprevalence was significantly associated with small ruminant seroprevalence but not with cattle seroprevalence. Annual incidence of human brucellosis exposure, measured by serological tests, was more than ten times higher than the annual incidence of reported clinical brucellosis cases. This indicates an under-reporting of human brucellosis cases, even if only a fraction of seropositive people have clinical symptoms. In conclusion, this study confirms the high seroprevalence of brucellosis in Kyrgyzstan and warrants rapid effective intervention, among others, by mass vaccination of sheep and goats but also of cattle.