DNA microarray analysis was conducted to investigate the transcriptional responses of the human monocytic leukemia cell line THP-1 to infection by Chlamydia trachomatis or Coxiella burnetii. RNA was isolated from mock infected cells and cells infected for 36 hours using TRIzol reagent. Biotinylated probes synthesized from RNA samples were hybridized to an Affymetrix U133A human genome chip consisting of 18,462 human gene probe sets. A total of 335 and 548 THP-1 genes were up- or downregulated at least twofold in cells infected with C. burnetii or C. trachomatis, respectively, when compared to uninfected cells. There was a high degree of overlap in transcriptional responses to infection with shared responses observed for 39 downregulated and 189 upregulated genes. Numerous pathogen-specific transcriptional responses were also observed. Quantitative RT-PCR and immunoblotting confirmed up- or down-regulation of a subset of THP-1 genes in response to infection by C. burnetii. This study provides insight into the host transcriptional responses to infection by Chlamydia and Coxiella that may affect the infectious cycle of each organism.