Plants respond to pathogen infection via a complex and integrated set of defenses driven by constitutive and induced responses. Parasitism by reniform nematode (RN) involves the formation of syncytia to provide nutrition for the female, and the events that occur at this feeding site may determine the degree of susceptibility of cotton plants to the nematode. In resistant G. arboreum accessions, between 6 to 12 days after penetration, complete necrosis occurs in the cells surrounding the nematode. The objectives of this study were to describe cotton root response after 9-days of RN infection and identify potential cotton root regulated genes under RN infection for reliable screening of nematode resistant plants. Four 3 week-old RN resistant or susceptible seedlings in 2-L jars containing autoclaved sand with MS salts were inoculated with 3,000 RN. The cDNA-AFLP and microarray approaches were performed to evaluate the host response at the transcriptome level