To study the responses of the host cell to chlamydial infection, differentially transcribed genes of the host cells were examined. Complementary DNA (cDNA) probes were made from messenger RNAs of HeLa cells infected with Chlamydia trachomatis and were hybridized to a high-density human DNA microarray of 15,000 genes and expressed sequence tags. C. trachomatis alters host cell transcription at both the early and middle phases of its developmental cycle. At 2 h after infection, 13 host genes showed mean expression ratios >/=2-fold. At 16 h after infection, 130 genes were differentially transcribed. These genes encoded factors inhibiting apoptosis and factors regulating cell differentiation, components of the cytoskeleton, transcription factors, and proinflammatory cytokines. This indicates that chlamydial infection, despite its intravacuolar location, alters the transcription of a broad range of host genes in diverse cellular pathways and provides a framework for future studies.