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, complete necrosis occurs in the cells surrounding the nematode. The objectives of this study were to describe cotton root response at the transcriptome level as a result of RN infection. Three 1 month-old RN resistant (A2-194) or susceptible (A2-128) seedlings in 500-cc pots containing autoclaved sand were inoculated with 5,500 RN. Mock-inoculation was included as control for each accession. Subtractive hybridization was performed to remove common mRNA between inoculated, mock inoculated, resistant and susceptible accessions. cDNA-AFLP was used to identify potential genes regulated during nematode infection.