Aphids have long been considered ‘stealthy’ herbivores that subvert a plant's induced defenses and manipulate its source-sink signaling, but these hypotheses are largely untested at a transcriptional level. We analysed gene expression in native tobacco plants (Nicotiana attenuata) infested with Myzus nicotianae aphids, without resorting to the use of clip-cages, with a cDNA microarray containing 240 defense-related N. attenuata genes. Using a hybridization scheme (‘ratio analysis’ and ‘state analysis’) broadly applicable in two-factor analyses, we examined how the aphids influenced source–sink relationships and determined if their feeding preference, apart from benefiting from the sink strength of young leaves, was associated with the expression of known plant defense genes. In contrast to the responses elicited by attack from tissue-feeding lepidopteran larvae and mesophyll-sucking insects, attack from phloem-feeding aphids elicited only weak responses. Similar to other herbivores, M. nicotianae feeding increased the expression of trypsin protease inhibitors (TPI), lipoxygenase, and xyloglucan-endotransglycosylase genes, and decreased small RUBISCO subunit and ubiquitin carrier protein transcripts. Aphid-specific changes included the up-regulation of glutamate synthase and the down-regulation of a germin-like protein. Aphids preferentially settled on younger leaves, which expressed more hydroperoxide lyase and TPI than did older leaves, suggesting that these genes, which mediate the synthesis of compounds reported to be toxic for aphids in other plant systems, are either not under transcriptional control or not important in this system. By identifying aphid-responsive genes, we have made a first step in identifying the ‘genes that matter’ in plant–aphid interactions.