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Despite past WHO/UNICEF led global yaws eradication efforts, the disease seems to persist. The true burden is however not known for comprehensive action. Ghana's data showed significant increase in notified cases since the 1970s. Recognizing limitations in routine data, we carried out a yaws treatment survey in 2008 in three purposively selected districts to establish the prevalence and learn lessons for renewed action. Of 208,413 school children examined, 4,006 were suspected yaws cases (prevalence 1.92 (95% CI: 1.86-1.98) percent). Of 547 schools surveyed, 13% had prevalence between 5% and 10% while 3% had prevalence above 10%. The highest school prevalence was 19.5%. Half of the schools had cases. The large sample allowed aggregating the school results by administrative levels. The lowest aggregated prevalences of 0.23%, 0.40%, and 0.64% were in the urban sub-districts of Asamankese, Oda, and Achiase, respectively, while the highest of 8.61%, 3.69%, and 1.4% were in rural Akroso, Mepom, and Aperade, respectively. In conclusion, the prevalence of yaws is high in some schools in rural, hard-to-reach areas of Ghana. Considering past global eradication efforts, our findings suggest yaws may be resurging for which programmatic action is needed.