Background: We wanted to elucidate the value of Borrelia antibodies in serum and cerebrospinal fluid (CSF) for the diagnosis of Lyme neuroborreliosis (LNB). Material and Methods: We analyzed the serological findings, by anti-flagellin assay, in 267 patients with neurological symptoms from the Stockholm area, where Lyme borreliosis is endemic. Results: In the 70 children with LNB, intrathecal Borrelia antibody production was diagnostic and found in 50 (71%). Sixteen (23%) showed an elevated antibody titer in serum only, and 4 (7%) had no serologic findings. Borrelia IgG in serum, with or without concomitant IgM, was a specific (98%), but insensitive (43%) marker of infection. Isolated, false-positive serum IgM titers were common and found in 10 of 67 children (15%) with viral meningitis, as well as in 28 of 111 (25%) with various neurological symptoms and normal CSF. The specificity of an isolated Borrelia IgM titer in serum was 81%, and the positive predictive value for Borrelia infection only 50% in our material. On the other hand, absence of antibodies in blood had a negative predictive value of 94%, which increased to 97% if also CSF findings were included. Conclusions: Intrathecal antibody production is strongly supportive of an LNB diagnosis. Conversely, isolated, elevated levels of Borrelia IgM in serum occur in up to one-fourth of children with various neurological complaints, and should be interpreted with caution, especially in non-endemic areas.