Androgens exert significant effects on the murine submandibular gland. Our objective in this study was to determine the nature and extent of testosterone regulation of gene expression in the female submandibular gland, and to explore the degree to which this control is the same as in male glands. Ovariectomized female BALB/c mice were treated with placebo- or testosterone-containing hormone pellets for 14 d. Glands were collected and total RNA was isolated. Samples were analyzed for differential expression of mRNA using CodeLink microarrays, and the data were evaluated using GENESIFTER. Testosterone significantly influenced the expression of over 500 genes, and while many (n = 214) of the genes were similarly differentially expressed in androgen-treated males, there were also many that were unique. These findings support our hypotheses that testosterone extensively influences gene expression in the female submandibular gland, and that the nature of this influence is variable between sexes.