【Abstract】 Objective To quantify the burden of Borrelia burgdorferi in different representative tissues from the murine host  by real time quantitative PCR(Q-PCR). Methods Low-passage B.burgdorferi was cultivated to logarithmic growth phase, and diluted to a concentration of 1×10⁵/ml for experimental use. To establish a B.burgdorferi-infected murine model, mice were injected 100 μl diluted culture intradermally in the back. After artificial infection was confirmed, mice were sacrificed at 12 d and 18 d post-infection in CO₂ box. Samples from skin, joint, heart and urine bladder were collected aseptically and frozen at -80 ℃, and total DNA was extracted. B.burgdorferi flaB was quantified by Q-PCR. Data were analyzed statistically to determine if bacterial burdens in various tissues showed a significant difference. Results spirochete burden was the highest in the urine bladder, medium in the skin and joint, lowest in the heart.  Conclusion There was significant difference among spirochete burden in various tissues. Spirochete burden in the tissue was not positively related to the severity of this tissue.