Abilities of B. burgdorferi to infect and induce illness is connected with immunopathogenic factors as: immunomodulatory elements of tick saliva abilities of B. burgdorferi to move in extracellular matrix, connecting and activation of proteolitic zymogen, inducing endothelium to production of adhesive molecules, chemokines and acute phase proteins. Important elements in pathogenesis and course of Lyme disease are organ tropism, producing by lymphocytes T proinflammatory cytokines (Th1 and Th2 profile), phagocytic abilities of infected organisms. In pathogenesis of chronic and recurrent cases difficult to treat is essential is survive of metabolic inactive bacteria, antigens B. burgdorferi as form "blebs", cystic L-form or insoluble complexes antigen-antibody or possibility of intracellular survive of B. burgdorferi. Tissue and organs damage is caused not only directly by B. burgdorferi antigens. Undoubtedly in the late stages there are immunologic disregulation and molecular mimicry. In some cases important are concommitant other infections. All this factors and results of therapy have influence on prognosis of Lyme disease. Knowledge of pathogenesis of Lyme disease has an important meaning in interpretation of laboratory tests and estimation of clinical signs and choosing of treatment.