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To establish the frequency of isolation of Borrelia burgdorferi sensu lato from blood of children with solitary erythema migrans (EM) in Europe, to determine the strains of the isolated borreliae and to compare the clinical course and the outcome of the disease according to positive and negative blood culture result.In the prospective study we included 134 consecutive patients younger than 15 years with solitary EM, referred to our institution in 1996 and 1997. One milliliter of blood was withdrawn before treatment and cultured in modified Kelly-Pettenkofer medium. Isolated borreliae were typed according to LRFP analysis. Patients were treated with either penicillin V or cefuroxime axetil for 14 days. The posttreatment course was surveyed by follow-up visits during 1 year.B. burgdorferi sensu lato was isolated in 12 of 134 (9%) patients. Eleven blood isolates were typed: 10 were found to be B. afzelii and 1 was Borrelia garinii. Comparison of blood culture-positive and -negative patients revealed no differences in pretreatment characteristics or in posttreatment clinical course. However, worsening of local and/or systemic signs and symptoms at the beginning of antibiotic therapy (Jarish-Herxheimer’s reaction) was identified more often in the blood culture-positive than in the blood culture-negative group (5 of 12 vs. 17 of 122, respectively;P = 0.0274).The isolation rate of B. burgdorferi sensu lato from the blood of children with solitary EM was 9%. The majority of the isolates were B. afzelii. Blood culture-positive patients treated with oral antibiotics were not at greater risk for unfavorable course of the disease than patients with negative blood culture result.