Nodding syndrome (NS) is a seizure disorder of unknown etiology, predominately affecting children aged 3-18 years in three sub-Saharan countries (Uganda, South Sudan, and Tanzania), with the primary feature of episodic head nodding. These episodes are thought to be one manifestation of a syndrome that includes neurologic deterioration, cognitive impairment, and additional seizure types. NS investigations have focused on clinical features, progression, and etiology; however, none have provided a population-based prevalence assessment using a standardized case definition. In March 2013, CDC and the Ugandan Ministry of Health (MOH) conducted a single-stage cluster survey to perform the first systematic assessment of prevalence of NS in Uganda using a new consensus case definition, which was modified during the course of the investigation. Based on the modified definition, the estimated number of probable NS cases in children aged 5-18 years in three northern Uganda districts was 1,687 (95% confidence interval [CI] = 1,463-1,912), for a prevalence of 6.8 (CI = 5.9-7.7) probable NS cases per 1,000 children aged 5-18 years in the three districts. These findings can guide the MOH to understand and provide the health-care resources necessary to address NS in northern Uganda, and provide a basis for future studies of NS in Uganda and in other areas affected by NS.