Apoptosis is an important process in a wide variety of different biological systems. In addition to caspases, recently, calpains, another family of proteases, have been found to be involved in apoptosis of many cell systems. This study is designed with the aims to evaluate the possible effect of Z-LLY-FMK (a calpain inhibitor) on intestine apoptosis after bile duct ligation in rats. Male Sprague-Dawley rats weighing 250-300 g were randomized to five groups (n = 6 in each group). Group 1 (CONTROL: C) underwent Sham operation and were simultaneously treated with the same amount of normal saline. Group 2 (CONTROL with DMSO: CDMSO) underwent Sham operation and were simultaneously treated with the same amount of dimethylsulfoxide (DMSO). Group 3 (Obstructive jaundice: OB) underwent common bile duct ligation without any other manipulation. Group 4 (Obstructive jaundice with Z-LLY-FMK: OBZLLY) underwent common bile duct ligation and were simultaneously treated with Z-LLY-FMK (dissolved in DMSO). Group 5 (Obstructive jaundice with ZFA-FMK: OBZFA) underwent common bile duct ligation and were simultaneously treated with ZFA-FMK (dissolved in DMSO). After 3 days, intestine tissue was harvested for apoptosis measurements. There was no significant difference between Sham operation group (C) and Sham operation with DMSO group (CDMSO) either in jejunum (P = 0.924) or in ileum (P = 0.996). When compared to Sham operation group (C), increased intestine apoptosis occurred in either jejunum (P < 0.001) or in ileum (P < 0.001) after common bile duct ligation (OB). After administration of Z-LLY-FMK (OBZLLY), the increased intestine apoptosis after common bile duct ligation (OB) was significantly diminished either in jejunum or in ileum (P < 0.001 and P < 0.001). Moreover, administration of ZFA (OBZFA) failed to show the same phenomenon in either jejunum (P = 0.993) or ileum (P = 0.485). There was a significant difference in intestine apoptosis in either jejunum (P < 0.001) or in ileum (P < 0.001) between OBZLLY group and OBZFA group. Significantly increased intestine apoptosis occurred after common bile duct ligation. The administration of Z-LLY-FMK could effectively diminish the intestine apoptosis after common bile duct ligation, whereas the administration of ZFA-FMK failed to show the same effect.