Objective To assess the variation and its significance of messenger ribonucleic acid(mRNA) expression of endothelial nitric oxide synthase (eNOS) in allografts of common carotid transplantation model in white rabbits. Methods To establish an animal model of common carotid transplantation in vivo, 30 rabbits were divided into four groups with random number table. Group A (n=3): autografts; group B (n=9): allografts with the least treated; group C (n=9): allografts treated by penicillin/streptomycin and preserved under room temperature; group D (n=9): allografts treated by penicillin/streptomycin and cryopreserved in liquid nitrogen. All the transplanted grafts were harvested 1-3 weeks later, then compared and evaluated the histomorphological variation and eNOS mRNA expression. Results The vascular structures of autografts in group A were kept approximately normal, only a few infiltration of inflammatory cells could be found. The structural variations of allografts in other trial groups behaved similarly as, intima proliferation in the 1st week, intima hyperplasia in the 2nd week, and both intima and media hypertrophy in the 3rd week. And also there seemed that luminal thrombosis could be found in all the allografts. Allografts in group B were destructed utmost the worst in all the groups. The expression of eNOS mRNA in allografts of group B was significantly less than that in other groups (Plt;0.05). Conclusion The down-regulation of eNOS mRNA expression might lead to intima hyperplasia and thrombosis of allografts.