Spirochetes Borrelia burgdorferi sensu lato, selected as antigens for Western blot analyses were isolated from cerebrospinal (strain 192 M) and from blood (strain Kc90) and identified by means of monoclonal antibodies and the polymerase chain reaction (PCR) as B. garinii and B. afzelii. Differences between B. garinii and B. afzelii are in the genotype of the surface protein OspA and OspB, internal flagellin (Fla II) and the main extracellular protein (MEP). The reaction of polyclonal antibodies in 918 serum specimens and 180 specimens of cerebrospinal fluid was investigated in IgG and IgM immunoblots in patients with neurological symptoms, arthritis and skin manifestations suspect of Lyme borreliosis. Confirmation of the immunoenzyme ELISA reaction by means of immunoblots in the acute stage of borreliosis, in clinically obscure cases, in herpetic infection, mononucleosis and leptospirosis revealed a higher sensitivity and specificity of Western blot. Proteins of B. garinii with a molecular weight of 94, 84, 66, 60, 56, 41, 39, 33, 29, 22, 18 and 14 kDa were detected in the reaction with monoclonal antibodies and immunoglobulins of patients suffering from barreliosis. The frequency and intensity of the reaction of these antigens differed markedly in sera of patients suffering from borreliosis and sera of patients who suffered from a different infection. The external surface antigen OspA, OspB, OspC and protein with 39 kDA are significant markers of borreliosis. The most frequently detected antigens in cross reactions with immunoglobulins against other pathogens are proteins P66, P60, P41 which are dominant immunogens of all types of borrelias and moreover a humoral response to them develops in the acute stage of the disease. In arthritis and neuroborreliosis a different in IgG immunoblots was found.