Background EphB2 is a transmembrane glycoprotein implicated in the regulation of cell growth, differentiation, and motility. It has been proposed as a tumor suppressor gene, and the role of EphB2 protein in tumorogenesis has been demonstrated. The aim of this study was to test the influence of mutation of A9 region in EphB2 gene in the prognosis of patients with sporadic CCR. Materials and Methods A total of 473 patients with colorectal cancer were included. A9 region in exon 17 of EphB2 was amplified using specific primer and analyzed using Genescan. All mutations were confirmed by direct sequencing. Results EphB2 mutation was detected in 13 of the 473 patients (2.7%). Mutation of EphB2 showed association with tumor site, 12 of 13 mutations were proximal tumors ( P  < 0.001). EphB2 mutation confers better prognosis in the adenocarcinoma group; 100% of patients carrying the mutation survived and were disease free after 72 months ( P  = 0.02 and 0.03, respectively). Conclusions Despite the low frequency of EphB2 gene, we got promising results. It would be very interesting to increase the population size to verify our results. If these findings are confirmed, EphB2 could help discriminate patients with adenocarcinoma with different prognosis and to improve the election of the most suitable treatment in each case.