We report the isolation of Borrelia lusitaniae from a 13-year-old female child presenting with a vasculitis syndrome. The patient was treated with doxycycline, 100 mg bid for 20 days, and is in remission after a follow-up of 2 years. These results should alert clinicians to the fact that B. lusitaniae may be pathogenic in humans, highlighting that patients may be seronegative or present with minimal positive antibody titres and clinical signs that are not specific for Lyme borreliosis. In order to prevent the occurrence of more serious disease manifestations via timely treatment, the analysis by molecular methods may be a useful approach when antibody titres are uninformative.