Baggio-Yoshinari syndrome is an emerging, tick-borne, infectious disease recently discovered in Brazil. This syndrome is similar to Lyme disease, which is common in the United States of America, Europe and Asia; however, Brazilian borreliosis diverges from the disease observed in the Northern Hemisphere in its epidemiological, microbiological, laboratory and clinical characteristics. Polymerase chain reaction procedures showed that Baggio-Yoshinari syndrome is caused by the Borrelia burgdorferi sensu stricto spirochete. This bacterium has not yet been isolated or cultured in adequate culture media. In Brazil, this zoonosis is transmitted to humans through the bite of Amblyomma and Rhipicephalus genera ticks; these vectors do not belong to the usual Lyme disease transmitters, which are members of the Ixodes ricinus complex. The adaptation of Borrelia burgdorferi to Brazilian vectors and reservoirs probably originated from spirochetes with atypical morphologies (cysts or cell-wall-deficient bacteria) exhibiting genetic adjustments, such as gene suppression. These particularities could explain the protracted survival of these bacteria in hosts, beyond the induction of a weak immune response and the emergence of serious reactive symptoms. The aim of the present report is to note differences between Baggio-Yoshinari syndrome and Lyme disease, to help health professionals recognize this exotic and neglected zoonosis.