Technical Abstract: While many studies have characterized the transcriptome of plants attacked by herbivorous insect pests, few have undertaken an examination of the genes affected by root pests. We have subjected maize seedlings to infestation by southern corn rootworm (SCR) Diabrotica undecimpunctata howardi and using a 57,000 maize microarray we have identified genes that are differentially expressed upon root infestation. We have found that 309 genes were induced >1.5 fold in maize roots while 237 were repressed <0.67 fold. Within induced genes, many pathogenesis related proteins were found including PR10s, chitinases, proteinase inhibitors, peroxidases and ß 1,3- glucanase. Additionally several WRKY transcription factors, often associated with responses to pathogens or herbivores, were found to be induced by SCR feeding. Using a shorter period of infestation, RNA from infested roots and their systemic uninfested shoots was isolated and the induction of several of these genes was confirmed by qRT-PCR. These genes were also tested for expression upon treatment of maize seedlings with the biotic stress hormones jasmonic acid or salicylic acid. The response to these hormones differed in the roots and the shoots and also differed among the specific SCR-induced gene tested. The evidence suggests that SA- and JA-dependent and independent signaling could be contributing to the transcriptome-level changes to maize roots and shoots in response to SCR infestation.