The reniform nematode (RN) Rotylenchulus reniformis is one of the major problems for cotton production in Lousiana, Mississippi, Alabama, and parts of Arkansas and Texas. In the absence of resistant cultivars, efforts are being made to transfer resistance from diploid cotton relatives (Gossypium arboreum, G. herbaceum, and G. longicalyx) to upland cotton G. hirsutum. But, little is know about the cotton root responses either in compatible and incompatible interaction with the RN.  In G. arboreum the RN is able to penetrate the roots of both resistant and susceptible accessions, but in the resistant ones, reproduction is very low or does not occur. It is hypothesized that what happens at the feeding site determines if the plant is resistant or susceptible to the RN. The objective of this study is to characterize the cotton root responses at the transcriptome level to RN infection. Oligonucleotide Microarray chips developed by the Wendel group at Iowa State University, Ames, IA were utilized to describe the gene response of cotton roots at 16 days past inoculation. Resistant (A2-194) and susceptible (A2-128) plants of G. arboreum were either inoculated with 37,000 nematodes or mock inoculated to obtain the four treatments evaluated in this study. A previous cDNA-AFLP study indicated that cellular transport, cell cycling and DNA processing resulted in more transcripts being expressed in the susceptible accession than in the resistant one. We hypothesize that the transcripts associated with those processes may be related to feeding site (syncytium) formation. On the other hand, the transcripts involved in processes that may be involved in resistance mechanisms, such as cellular rescue, defense and transcription, were more abundant in the resistant accession. The objective of this study is to determine if our hypothesis will be corroborated by microarray analyses.