BACKGROUND:Information on the etiology of Lyme neuroborreliosis (LNB) in children in Europe and the influence of Borrelia burgdorferi sensu lato species isolated from cerebrospinal fluid (CSF) on clinical presentation of LNB in children are limited. METHODS:The study was monocentric. During its 17-year period, children younger than 15 years with presentation suggestive of LNB or confirmed Lyme borreliosis that had B. burgdorferi sensu lato isolated from CSF and had species of B. burgdorferi sensu lato identified by pulsed-field gel electrophoresis were included. Demographic and medical data were compared for children infected with Borrelia garinii to those infected with Borrelia afzelii. RESULTS:One hundred and fifty-three children had B. burgdorferi sensu lato isolated from CSF. In 71/113 (62.8%) and 42/113 (37.2%) patients, B. garinii and B. afzelii, respectively, were identified. Patients infected with B. garinii did not report symptoms suggestive of central nervous system (CNS) involvement or any other symptoms more often than patients infected with B. afzelii. Compared with children infected with B. afzelii, children infected with B. garinii had erythema migrans less often (18.3% vs. 45.2%) but had positive meningeal signs (69.0% vs. 38.1%), CSF lymphocytic predominance (97.1% vs. 75.0%), and elevated albumin CSF/serum quotient (80.6% vs. 50.0%) more often. CONCLUSIONS:In Slovenia, LNB in children is more often caused by B. garinii, followed by B. afzelii. The clinical picture of LNB in children caused by B. garinii is not more often suggestive of CNS involvement, but CNS inflammation is more pronounced in children infected with B. garinii, compared with children infected with B. afzelii.