The two strains of inbred mice, BALB/c and C57BL/6, are widely used in pre-clinical psychiatry research due to their differences in stress susceptibility. Gene profiling studies in these strains have implicated the inflammation pathway as the main contributor to these differences. We focused our attention on female mice and tested their response to 5- or 10-day exposure to restraint stress. We examined the stress induced changes in the regulation of 11 inflammatory cytokine genes and 12 glutamate receptor genes in the hippocampus of female BALB/c and C57BL/6 mice using quantitative PCR. Elevated proinflammatory cytokine genes include Tumor Necrosis Factor alpha (TNFa), nuclear factor kappa-light-chain-enhancer of activated B cells (NFKB), Interleukin 1 alpha (IL1a), Interleukin 1 receptor (IL1R), Interleukin 10 receptor alpha subunit (IL10Ra), Interleukin 10 receptor beta subunit (IL10Rb), and tumor necrosis factor (TNF) super family members. Our results show that BALB/c and C57BL/6 mice differ in the genes induced in response to stress exposure and the level of gene regulation change. Our results show that the gene regulation in female BALB/c and C57BL/6 mice differs between strains in the genes regulated and the magnitude of the changes.