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The aim of this study was to assess the potential clinical implications of Chlamydophila pneumoniae in patients with acute and chronic arthritic diseases and to investigate whether blood monocytes might reflect a concomitant synovial or persistent systemic infection. C. pneumoniae was investigated with advanced PCR and reverse transcriptase (RT) PCR techniques targeting different genes and combined with cell line cultures, in synovial fluid (SF) and peripheral blood mononuclear cell (PBMC) specimens collected from 28 patients with arthritis. Five out of twenty-eight patients (17.8%) were found to have C. pneumoniae DNA in either SF or PBMC specimens. Their diagnosis was reactive arthritis (ReA), S.A.P.H.O syndrome, psoriatic arthritis, undifferentiated oligoarthritis (UOA) and ankylosing spondylitis (AS). Specimens from patients with UOA and AS had also mRNA transcripts but those from AS yielded C. pneumoniae growth after co-culture. Moreover, C. pneumoniae DNA levels measured by Real-Time PCR (LightCycler) were higher in PBMC specimens compared to those found in SF at the end of antibiotic treatment. C. pneumoniae may have a role as triggering factor also in chronic arthritides including AS. The combined use of culture and molecular tools increases detection rates and improves the overall sensitivity, suggesting their potential use to detect C. pneumoniae. The different kinetics of bacterial DNA at both peripheral and synovial levels should be taken into consideration when monitoring and evaluating the effectiveness of antibiotic treatment. © 2010 Springer-Verlag.