In November 2010, the Ministry of Health of the proposed nation of South Sudan requested CDC assistance in investigating a recent increase and geographic clustering of an illness resulting in head nodding and seizures. The outbreak was suspected to be nodding syndrome, an unexplained neurologic condition characterized by episodes of repetitive dropping forward of the head, often accompanied by other seizure-like activity, such as convulsions or staring spells. The condition predominantly affects children aged 5-15 years and has been reported in South Sudan from the states of Western and Central Equatoria and in Northern Uganda and southern Tanzania. Because of visa and security concerns, CDC investigators did not travel to South Sudan until May 2011. On arrival, a case-control study was conducted that included collecting exposure information and biologic specimens to assess the association of nodding syndrome with suspected risk factors. A total of 38 matched case-control pairs were enrolled from two different communities: Maridi and Witto. Overall, current infection with Onchocerca volvulus diagnosed by skin snip was more prevalent among the 38 case-patients (76.3%) than the controls (47.4%) (matched odds ratio [mOR] = 3.2). This difference was driven by the 25 pairs in Maridi (88.0% among case-patients, 44.0% among controls, mOR=9.3); among the 13 pairs in Witto, no significant association with onchocerciasis (known as river blindness) was observed. Although onchocerciasis was more prevalent among case-patients, whether infection preceded or followed nodding syndrome onset was unknown. Priorities for nodding syndrome investigations include improving surveillance to monitor the number of cases and their geographic distribution and continued work to determine the etiology of the syndrome.