We used a highly quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) assay system to define the steady-state levels of mRNA encoding a large panel of soluble mediators of inflammation in synovial tissues from patients with chronic arthritis infected with Chlamydia trachomatis versus C. pneumoniae. RNA/cDNA was prepared from synovial biopsies of 4 patients with chronic arthritis and joint infection with C. trachomatis, 6 with C. pneumoniae at that site, 3 uninfected healthy controls, and 3 patients with undifferentiated oligoarthritis (UO) who were PCR negative for all organisms assayed. Real-time RT-PCR was used to assess relative mRNA levels from 12 cytokine and 2 chemokine genes (IL-1alpha, IL-1beta, IL-2, IL-4, IL-5, IL-8, IL-10, IL-12p35, IL-12p40, IL-15, IFN-gamma, TNF-alpha, MCP-1, RANTES). Input loading was normalized to 18S rRNA. Data were obtained for each mRNA from each sample in triplicate in comparison to the same mRNA level in the controls. In most C. trachomatis infected synovial tissue samples, high levels of IL-10 mRNA were present, with less mRNA for IL-8, IL-15, IFN-gamma, and TNF-alpha. Synovial tissues from chronic arthritis patients with synovial C. pneumoniae showed significant levels of mRNA solely for IL-8 and IL-1beta. All other cytokine messengers assessed in each sample from each patient group were at or near control level. One patient with C. pneumoniae showed a high transcript level for RANTES, and one patient with C. trachomatis showed a high transcript level for MCP-1. No patient with UO showed elevated messenger level for any cytokines assayed, but RANTES mRNA was elevated in each. Our data suggest that while both C. trachomatis and C. pneumoniae have been associated with inflammatory joint disease, each elicits a somewhat different steady-state profile of mRNA encoding relevant cytokines and chemokines during chronic infection of synovial tissue. Precisely how these differing profiles relate to clinical aspects of synovial inflammation will require further study, but the observations confirm and extend data indicating potentially important differences in the pathobiology of these 2 bacterial species.