We previously generated a double knockout mutant (act/aopB) of a diarrheal isolate SSU of A. hydrophila, in which the genes encoding Aeromonas outer membrane protein B (AopB), a structural component of the type III secretion system (T3SS), and a type II (T2)-secreted cytotoxic enterotoxin gene (act) were deleted. This mutant exhibited minimal virulence in mice, compared to animals infected with wild-type (WT) A. hydrophila. Based on microarray analyses, WT A. hydrophila altered the expression of 434 and 80 genes in murine macrophages (RAW 264.7) and human colonic epithelial cells (HT-29), respectively. Approximately half of these gene expression alterations were abrogated when host cells were infected instead with the act/aopB mutant. In this study, we used microarrays to examine early host transcriptional responses in spleens of mice infected for 3h with WT A. hydrophila or its act/aopB mutant. Our data indicated that expression of 221 genes was altered (158 up-regulated and 63 down-regulated) in spleens of WT bacteria-infected animals. There were 21 genes that were consistently more highly expressed in WT A. hydrophila-infected mice, compared to mice infected with its act/aopB mutant. Ten of these genes were either induced to a lesser extent (e.g., interleukin-6, macrophage inflammatory protein-2, and cyclooxygenase-2), not altered at all (e.g., killer cell lectin-like receptor subfamily B member A), or down-regulated (e.g., cytochrome P450) in animals infected with A. hydrophila, compared to phosphate-buffered saline-infected control animals, when the mutant was used instead of the WT. We verified the microarray results at the transcript level by performing real-time reverse transcriptase-polymerase chain reaction on selected genes and at the protein level by enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry. This is the first study demonstrating in vivo gene regulation in mice infected with A. hydrophila and the contribution of virulence factors and host responses to the disease process.