Many approaches were made in recent years to establish urine PCR as a diagnostic tool for Lyme borreliosis, but results are contradictory. In the present study, a standardized protocol spiking urine from healthy donors with a defined amount of whole Borrelia or Borrelia DNA was established. The development of a nested real-time PCR targeting ospA enabled a highly sensitive and quantitative analysis of these samples. We show the following. (i) Storage of spiked urine samples for up to 6 months at ؊20°C had no negative effect on spike recovery. (ii) Centrifugation of 10 ml of urine at 40,000 ؋ g for 30 min resulted in a concentration of both spikes, i.e., whole Borrelia and DNA. (iii) The inhibition of DNA spike recovery in 48% (11 of 23 samples) of urine samples tested could be attributed to nuclease activity. This was abrogated by alkalizing the urine or by working with the samples on ice. Despite optimized conditions, analysis of urine samples of 12 patients with erythema migrans, the clinical stage considered to be associated with the highest bacterial load, revealed a positive result in only one sample. All 12 samples were negative by an alternative PCR targeting flagellin. The results of our study support doubts that urine is a suitable material for diagnosis of Lyme borreliosis.Diagnosis of Lyme borreliosis (LB) is currently based on clinical criteria confirmed by serological tests. However, serology has a number of limitations, such as serological crossreactivity, the delayed production of antibodies in early stages of LB, and an inability to distinguish between ongoing and previous infections, due to the persistence of antibodies. In patients with ongoing or recurring symptoms after antibiotic therapy, it is often impossible to definitely attribute clinical symptoms to a persistent infection with Borrelia burgdorferi sensu lato, the causative agent of LB. A way out of this dilemma might be the direct detection of this pathogen in clinical samples, such as the detection of Borrelia DNA by PCR. The use of urine as a sample material is an attractive approach, since urine is obtained without invasive procedures.Since 1991, when the detection of Borrelia DNA in urine was shown for the first time by Goodman et al. (14), many studies have been carried out (for reviews, see references 11, 19, and 29). A comparison between the different reports is nearly impossible because of significant differences in patient selection, study design, and DNA extraction and PCR methods. Nevertheless, a meta-analysis of urine PCR assays for diagnosis of LB showed an overall sensitivity of 68% (range, 13 to 100%) and a specificity of 99% (range, 95 to 100%) (11).Even when comparing only reports on urine of patients with erythema migrans (EM) who clearly have an active infection, detection of Borrelia DNA in urine ranged between 13% and Ͼ90% (1,5,20,25,28,30). A caution was issued by Brettschneider et al., who were not able to confirm the presence of Borrelia DNA in the 27% PCR-positive urine speci-