Plants discriminate among pollen grains that land on the stigma surface, providing compatible pollen with the nutrients and signals required to proceed in pollination, and in many species, recognizing and inhibiting foreign pollen adhesion, hydration, germination and invasion. Much of the stigma machinery involved in these processes remains unknown. It is likely that the expression of a stigma-specific gene program confers specialized structural and functional properties. Here we used microarray technology and cDNA subtraction to build a profile of candidate stigma genes that facilitate early pollination events. Of over 24,000 Arabidopsis genes probed, we identified 11,403 genes expressed in stigma tissue; 317 of these were not expressed in control tissues. Analysis of the stigma transcriptome demonstrated a unique transcriptional profile. Functional specialization of the stigma for extracellular interactions is reflected by an increased number of stigma-specific and stigma-expressed genes involved in sculpturing the cuticle and cell wall, lipid metabolism, as well as genes potentially involved in pollen–stigma interactions.