Nodding syndrome (NS) is a neurologic disorder of unknown etiology characterized by vertical head nodding that has affected children aged 5-18 years in East Africa. Previous studies have examined relationships with biological agents (e.g., nematodes, measles, and fungi), but there is limited data on the possible contributions of neurotoxic environmental chemicals frequently used as pesticides/insecticides to the development and progression of this disorder. We examined the levels of persistent organochlorine pesticides (OCPs) in children (5-18 years old) from Kitgum District, Northern Uganda. These children previously lived in internally displaced people's (IDP) camps, where they were exposed to various health risks, including contaminated food and water. Exposure to OCPs through contaminated food and water is postulated here as a potential contributor to NS etiology. We analyzed serum (n = 75) and urine (n = 150) samples from children diagnosed with NS, and from seizure-free household controls (HC), and community controls (CC). Samples were extracted using solid-phase extraction (SPE) and extracts were analyzed for OCPs using gas chromatography with a triple quadrupole mass spectrometry (GC-MS/MS). Mean levels of total (∑) ∑OCPs in serum samples from NS, HC and CC subjects were 23.3 ± 2.82, 21.1 ± 3.40 and 20.9 ± 4.24 ng/mL, respectively, while in urine samples were 1.86 ± 1.03, 2.83 ± 1.42, and 2.14 ± 0.94 ng/mL, respectively. Correlation and linear regression analysis indicated that potential markers for ∑hexachlorocyclohexanes (HCHs), ∑chlordane compounds (CHLs), ∑endosulfan and ∑dichlorodiphenyltrichloroethanes (DDTs) were γ-HCH, heptachlor-exo-epoxide, endosulfan-α and p,p'-DDD in NS cases while in controls were α -HCH, heptachlor, endosulfan-α and p,p'-DDE, respectively. Since, in some instances, higher OCP levels were found in controls vs. NS cases, we conclude that exposure to organochlorine pesticides is unlikely to be associated with the etiology of NS.