Motivation: Gene expression patterns can be useful in understan-ding the structural organization of the brain and the regulatory logic that governs its myriad cell types. A particularly rich source of spa-tial expression data is the Allen Brain Atlas (ABA), a comprehensive genome-wide in situ hybridization study of the adult mouse brain. Here we present an open-source program, ALLENMINER, that searches the ABA for genes that are expressed, enriched, patterned, or graded in a user-specified region of interest. Results: Regionally enriched genes identified by ALLENMINER accurately reflect the in situ data (95-99 % concordance with manual curation) and compare to regional microarray studies as expected from previous comparisons (61-80 % concordance). We demonstrate the utility of ALLENMINER by identifying genes that exhibit patterned expression in the caudoputamen and neocortex. We discuss gene-ral characteristics of gene expression in the mouse brain and the potential application of ALLENMINER to design strategies for specific genetic access to brain regions and cell types. Availability: ALLENMINER is freely available on the Internet at