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Yaws, a non-venereal treponemal disease, is targeted for eradication by 2020 but accurate epidemiological data to guide control programs remain sparse. The Solomon Islands reports the second highest number of cases of yaws worldwide. We conducted a cluster randomized survey of yaws in two provinces of the Solomon Islands. One thousand four hundred and ninety-seven (1,497) children 5-14 years of age were examined. Clinical signs of active yaws were found in 79 children (5.5%), whereas 140 children (9.4%) had evidence of healed yaws lesions. Four hundred and seventy (470) (31.4%) children had a positive Treponema pallidum particle agglutination assay (TPPA). Two hundred and eighty-five (285) children (19%) had a positive TPPA and rapid plasma regain assay. Risk of yaws increased with age and was more common in males. The prevalence of yaws at village level was the major risk factor for infection. Our findings suggest the village, not the household, should be the unit of treatment in the World Health Organization (WHO) yaws eradication strategy.