Viliuisk encephalomyelitis (VE) is an endemic neurological disease in Northeastern Siberia and generally believed to be a chronic encephalomyelitis of unknown origin. We investigated 17 patients with a clinical diagnosis of VE within the Viliuiski region of Sakha (Yakutian) Republic to explore the core clinical syndrome of chronic VE and subsequently whether VE is caused by Borrelia burgdorferi infection. We found a chronic myelopathy as the core of the syndrome, often following an acute phase with a meningo-radiculo-neuropathy, suggestive of chronic neuroborreliosis. A search for inflammatory parameters in a larger cohort in blood (39 VE patients and 41 controls) and CSF samples (10 VE patients and 7 controls) excluded an ongoing chronic infection, but revealed evidence for an immunological scar or a chronic inflammatory ("autoimmune") response in the CSF. In addition, we detected signs of a previous exposure to Borrelia burgdorferi antigens in a subset of chronic VE patients with positive serological results using ELISA/immunoblot in 54/10% and 22/0% of VE patients and controls, respectively (p values of 0.003/0.034; Fisher's exact test). However, CSF analyses did not show a link between exposure or at least immunological reaction against Borrelia and the risk of suffering from VE. Our data provide the first evidence of the presence of Borrelia burgdorferi or similar pathogens in Northeastern Siberia, but do not support a causative role of these pathogens in the aetiopathogenesis of VE.