We aimed to investigate prevalence of potential risk factors, and associations between risk factors and active trachoma in southern Sudan. Surveys were undertaken in ten sites and children aged 1-9 years examined for trachoma. Risk factors were assessed through interviews and observations. Using ordinal logistic regression, associations between severity of active trachoma and risk factors were explored. Trachomatous inflammation-intense (TI) was considered more severe than trachomatous inflammation-follicular (TF). A total of 7,418 children were included in the analysis. Risk factors and prevalences were unclean face, 52.3%; face washed less than twice daily, 50.8%; water collection > 30 minutes, 38.1%; absence of latrines, 95.4%; garbage disposal within 20 m, 74.4%; cattle ownership, 69.2%; and flies, 83.3%. After adjusting for age and sex, unclean face, less frequent face washing, cattle ownership, and increasing fly density were found to be independently associated with severity of active trachoma. Our study suggests that facial hygiene and environmental sanitation are priority trachoma-control interventions in southern Sudan.