Background: Toxoplasma gondii is genetically diverse and different genotypes differ markedly in phenotype. The present study aims to define transcriptional patterns and biological processes that characterize host response to distinct strains of T. gondii. Methods: We conducted a time course study of gene expression microarray in mice during acute infection (days 1 to 7) with the highly virulent type I (GT1 strain), intermediately virulent type II (PTG strain) and non-virulent type III (CTG strain) parasites. Results: Overall, the number of genes affected increased from day 1 to day 5, and decreased on day 7. However, type III and type II infections up-regulated more genes than did type I at the very early phase, whereas type I infection up-regulated more genes at the late phase. Gene ontology (GO) analysis showed that the genes related to inflammatory and immune response were mostly affected and the majority were up-regulated, with type III infection inducing a higher degree of change and affecting more genes than did type I at the early phase. However, this pattern was reversed at the late phase. The change of expression during type II infection was between that of types I and III. Many genes associated with inflammatory and immune responses showed bimodal effects, with the first peak expression mostly at day 3 and then a second peak expression mostly at day 5. Several differentially expressed genes, including INF-γ, iNOS, CXCL10/IP-10, and numerous immunity-related GTPases (IRGs) and guanylate-binding proteins (GBPs) were previously experimentally confirmed important host factors in controlling T. gondii infection. Bioinformatic analysis of biological pathways enriched during infection revealed upregulation of pathways relating to cell-mediated immunity and the inflammatory response during all three infection types, though such enrichment was most expansive and pronounced during type I infection, and much less pronounced during type III infection. Conclusions: The findings in our study revealed dynamic differences of gene expression and different pathways of immune response in mice infected with three distinct strains of T. gondii.