Borrelia burgdorferi is highly susceptible to antibiotic treatment and the majority of patients profit from this treatment. Antibiotic selection, dose and route of administration, and duration of therapy for Lyme disease depend on the patient's clinical manifestations and stage of disease, age, pregnancy status, as well as the presence of other concomitant diseases and/or allergies. Despite an appropriate antibiotic therapy, about 10-20% of patients may show persistent or recurrent symptoms ("post-treatment Lyme disease syndrome").In the present paper we will briefly discuss the post-exposure prophylaxis, before going on to talk over the current therapeutic approach regarding the management of Lyme disease according to the stage of disease/clinical manifestations. Finally, we will discuss the main treatment-related phenomenon, the Jarisch-Herxheimer reaction, and the treatment modalities for special categories of patients, namely pregnant women, subjects suffering from post-treatment Lyme disease syndrome, possible Borrelia-associated skin manifestations, coinfections and Baggio-Yoshinary syndrome.