OBJECTIVE: Bacteria play a crucial pathogenetic role in reactive arthritis (ReA) and other forms of spondyloarthropathy (SpA) and in Lyme arthritis. Although there is evidence of local persistence of bacterial antigens no definitive method revealing microbes in peripheral joints has been established. We detected DNA of individual bacteria in synovial material by PCR. Applying molecular technology we screened simultaneously for 8 bacterial genomes in arthritis and sacroiliitis. METHODS: Sacroiliac (SI) biopsy specimens taken from the SI joint of 8 patients with ankylosing spondylitis (AS, n = 5) and undifferentiated SpA (uSpA, n = 3) by computed tomography guided biopsy were investigated for presence of bacterial DNA. Similarly, synovial membrane samples obtained by office arthroscopy from 15 patients with ReA (n = 5), uSpA (n = 3), undifferentiated oligoarthritis (uOligo, n = 3), and rheumatoid arthritis (RA, n = 4) were screened. Nested PCR was performed for DNA of the following bacteria: Chlamydia trachomatis, C. pneumoniae, Yersinia enterocolitica, Salmonella enteritidis, Campylobacter jejuni, Shigella flexneri, Klebsiella pneumoniae, and Borrelia burgdorferi. RESULTS: No bacterial DNA was found in the SI biopsies of patients with uSpA and AS. DNA of B. burgdorferi (n = 2) and C. trachomatis (n = 1) was detected in 3 patients with uOligo, but not in patients with ReA or RA. DNA of other microbes including K. pneumoniae was not found. Patients' mean disease duration was 5.3 years (2 mo-8.4 yrs). CONCLUSION: We found bacterial DNA in peripheral joints of patients with uOligo, while in patients with ReA, AS, and uSpA no bacterial DNA was detected in peripheral or SI joints. The failure to detect bacterial DNA in patients with SpA suggests autoimmune mechanisms operate in later stages of disease.