Objective To investigate the joint effects of selective digestive decontamination (SDD) and glutamine (Gln) on preventing intestinal bacterial translocation of orthotopic piggyback liver transplantation and to observe the incidence of postoperative pneumonia in rabbit. Methods Thirty rabbits received orthotopic piggyback liver transplantation and were randomly divided into three groups (SDD group, SDD+Gln group and control group). Mixed emulsion of tobramycin, polymyxin E and nystatin were given to the rabbits in SDD group. Same dosage of the above components plus Gln were given to the rabbits in SDD+Gln group. Samples of portal vein blood, ileum tissue and lung tissue were obtained in each group at different phases during and after operation, the pathological changes of ileum tissue, the bacterial translocation in blood of portal vein and the incidence of postoperative pneumonia were detected. Results The mixing section area of intestinal blood capillaries in SDD+Gln group was smaller compared with control group (P＜0.05， P＜0.01) and SDD group (P＜0.05) while the portal vein was obstructed for 15, 30 and 45 min, and after the operation, respectively. The length of ileum villus in SDD+Gln group was longer than that in control group (P＜0.05) and in SDD group (P＜0.05) before the portal vein was obstructed, but the length of ileum villus in control group gradually became longer and eventually exceeded that in SDD+Gln group at the time of 45 min after the portal vein was obstructed (P＜0.05). After the operation, the length of ileum villus in SDD+Gln group was significantly longer than that in SDD group (P＜0.05) and control group (P＜0.01). At the time of 45 min after the obstruction of portal vein and 30 hours after operation, the positive rate of cultured bacterial in the blood of portal vein in SDD+Gln group was significantly lower than that in control group (P＜0.05, P＜0.01). The incidence of postoperative pneumonia in SDD+Gln group and SDD group were significantly lower than that in control group (P＜0.05,P＜0.01). Conclusion Gln could nourish intestinal epithelium of mucous membrane.When combined with SDD, it could decreased the incidence of intestinal bacterial translocation occurred during the obstruction of portal vein and after operation, so as to decrease the incidence of postoperative pneumonia.