Cathepsin E is an endolysosomal aspartic proteinase predominantly expressed in cells of the immune system and has been implicated in various physiological and pathological processes. Because of physiological substrates of cathepsin E have not yet been identified, however, the physiological significance of this protein still remains speculative. To better understand the physiological significance of cathepsin E in the mammary gland, we investigated the effect of the deficiency of this protein on the gene expression profile of the tissue. Here we used mammary glands derived from multiparous and non-pregnant 11-month-old syngenic wild-type (CatE(+/+)) and cathepsin E-deficient (CatE(-/-)) mice for extraction of total RNA from each tissue and subsequent mRNA amplification, DNA fragmentation, and hybridization with cDNA mixroarray chips. A total of 654 genes were identified as overexpressed (>2-fold) in CatE(-/-) mammary glands compared with CatE(+/+) counterparts. These included genes related to signal transduction, immune responses, growth factor activity, and milk proteins, which occupied a large portion of the gene fragments identified as overexpressed. In contrast, a total of 665 known genes were identified as underexpressed in the mammary gland of CatE(-/-) mice compared with CatE(+/+) counterparts. These included genes related to cytoskeleton, cell differentiation, cell cycle arrest and apoptosis, which occupied the majority of the gene fragments identified as underexpressed. The results thus suggest that cathepsin E in mammary glands plays a crucial role in the regulation of proteins involved in signaling, development, differentiation and proliferation in the mammary gland.