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Purpose: To determine baseline prevalence data and collect related risk factor information for trachoma before implementation of trachoma control measures in Southern Sudan. Methods: A total of 1,281 people (536 male and 745 female; age 1mo-72yrs, mean 20.1yrs) in 193 households were examined for signs of trachoma. The households were selected on the basis of accessibility, due to the ongoing civil war and after negotiation with the local authorities. Upper eyelid eversion was performed on all individuals of a household. Trachoma was graded using the World Health Organization simplified grading scheme. An active case of trachoma was determined by the presence of TF or TI in at least one eye. A clean face was defined as a face without any ocular or nasal discharge. Data was analyzed using the EpiInfo 2000 software. Results: The prevalence of active trachoma in children ? 10 year of age was 54.5%. Trichiasis was present in 17.7% of females 15 years or older. Trachomatous scarring was present in 19.8% of people over the age of 30 years. Overall, 53.3% of all examined individuals had at least one sign of trachoma in one eye. There was no statistically significant difference in the prevalence of trachoma between females (55.3%) and males (50.6%)({chi}2 = 2.63, p0.05). Children ? 10 years of age without clean faces were 1.4 (95%CI, 1.14, 1.63) times more likely to have active trachoma in at least one eye than children with clean faces. Conclusions: Previously, there were only anecdotal reports of trachoma in Southern Sudan, but this survey demonstrates that trachoma is a serious public health problem in this area. The presence of the observed high prevalence of trachoma underscores the need for the implementation of trachoma control measures for the forgotten and highly disadvantaged population in Southern Sudan.