Corn has shown different degrees of positive response to inoculation with the nitrogen- fixing bacteria of the genera Azospirillum. Part of it has been attributed to the plant genotypic variation, including the root exudates, that are used by the bacteria as energy source. In this study, we grew two corn hybrids that differ for their response to Azospirillum, to investigate the effect of different exudates profiles on the bacteria growth and nitrogenase activity. Employing high performance liquid chromatography, we identified nine amino acids (asparagine, aspartic acid, serine, glutamic acid, valine, phenylalanine, threonine, tryptophan and alanine), six sugars (glucose, sucrose, xylose, arabinose, fructose and galactose) and four organic acids (citrate, malate, succinate and fumarate). The less responsive corn genotype showed reduced plant growth (root volume, shoot dry mass and shoot N content), a lower concentration of Azospirillum cells within the root tissues, a higher content of asparagine and glucose and a reduced amount of metabolites that serve as bacterial energy source (all organic acids + five sugars, excluding glucose). The genotypes did not interfere in the ability of Azospirillum to colonize the substrate, but the metabolites released by the less responsive one reduced the nitrogenase activity.