This study analyzed the onset of lipid peroxidation (LPO) in neuroborreliosis and the effects of ceftriaxone therapy on LPO. Twenty-two patients with early neuroborreliosis and 22 healthy subjects were studied. LPO in the cerebrospinal fluid (CSF), as well as the plasma and urine was estimated by the levels of reactive aldehydes: 4-hydroxynonenal (4-HNE), 4-hydroxyhexenal, malondialdehyde, and 4-oxononenal, F2-isoprostanes and A4/J4-neuroprostanes (NPs). The plasma level of 4-HNE-protein adducts arachidonic acid (AA), docosahexaenoic acid (DHA) and vitamin E was determined. Additionally, enzymatic activities of phospholipase A2 (PLA2), platelet-activating factor acetylhydrolase (PAF-AH) and glutathione peroxidase (GSH-Px) were determined. A decrease of AA, DHA levels and GSH-Px activity in plasma was associated with a significant increase of aldehydes in the CSF, plasma and urine. Similarly, the increase of F2-isoprostanes and NPs in the CSF and plasma was associated with the decreased activity of PLA2 and PAF-AH. Ceftriaxone therapy cured patients and reduced the levels of F2-isoprostanes, NPs and reactive aldehydes. However, the activities of PLA2 and PAF-AH increased. Pathophysiological association of neuroborreliosis with systemic LPO was revealed. Effective antibiotic therapy attenuated LPO. Biomarkers of LPO could be useful to monitor the onset of neuroborreliosis and show the effectiveness of pharmacotherapy.