We have screened 91 migratory birds representing 32 species during the autumn of 2003 for the presence of the zoonotic pathogens Borrelia and Chlamydophila. Using polymerase chain reaction (PCR), B. burgdorferi sensu stricto was detected in cloacal swabs and, in two causes, also in throat swabs in 8 individuals (8.7 %) representing 7 birds species; B. garinii and B. afzelii were not detected. C. psittaci was detected only in cloacal swabs; 6 birds (6.6 %) from four species were found to be positive. The PCR products were sequenced and the sequences were compared phylogenetically with the gene sequences of 14 Chlamydophila strains retrieved from nucleotide databases; although the sequenced DNA was only 110 bp long, all obtained sequences created a new cluster with sublines branching from a position close to the periphery of the genus. All tested samples appear distinct within the known species and were most similar to C. felis or C. abortis.