In the wake of controversies surrounding the usefulness of PCR in the diagnostics of borreliosis, the aim of the presented study was to monitor the presence of B. burgdorferi s.l. in dogs with clinical borreliosis in the course of relevant treatment. The monitoring was based on detecting borrelia's DNA before- (study I), during- (study II), and after completion of the therapy (study III). In addition, to rule out possible coinfections, the dogs' blood was examined for the presence of anaplasma, babesia and rickettsia. Blood samples taken from 11 dogs, with clinically detected borreliosis, were used for obtaining DNA for PCR. Positive results of PCR, with primers complementary to the fla gene, indicating the presence of DNA of B. burgdorferi s.l., were noted, in study I, in the blood of 7 dogs (63.6% dogs), in study II in 3 dogs, while in study III all blood samples were negative. In 6 out of 7 PCR+, the first study was carried out during week 1. Therefore, the PCR method is useful for monitoring early canine infections with spirochetes B. burgdorferi s.l. In all positive samples, subjected to PCR-RFLP, it was the case of a single genospecies, i.e. B. burgdorferi sensu stricto. Studies for the presence of DNA of Babesia sp., as well as DNA of Ricettsia helvetica, were negative in all samples. Anaplasma phagocytophilum DNA was detected in the blood of a single dog, and only in study I. The same dog also proved positive for the presence of borrelia DNA. Co-occurrence of both pathogens did not disturb the clinical picture of borreliosis, and the administered treatment was also effective for the mixed infection.