Aim To measurement the inhibitory effect of Momordicin on the activity of caspase 3 and apoptosis of myocardium in BALB/C mice with coxsackievirus B3 myocarditis. Method Momordicin was purificated from Momordica charantia L by our previous reported methods. Four group animals were used in this experiment, such as disease group (DG), normal group (NG), Momordicin group (MG), and Momordicin therapy group (MTG). Five animals were killed at the 3rd,the 7th,and the 14th days in each group, and all were killed at the 21st day. According to the method of Calbiochem Company, the activity of caspase 3 from the heart of BALB/C mice was measured, and apoptosis was measured by terminal transferase mediated DNA nick end labeling assay (TUNEL, the method provided by Oncogene Company). Results ①The activity of caspase 3 were measurable at the 7th day in the DG (0.63±0.21 pmol/min, n=5). The activity of caspase 3 at the 14th day (10.9±1.5 pmol/min, n=5) and the 21st day (12.6±1.3 pmol/min, n=5) are higer than the 7th day, and the activity of the 21st was higher than 14th day (p<0.05). ②Only a animal has the activity of caspase 3 at the 21st day (0.41 pmol/min) in the HTG, no caspase 3 activity were detected in the animals of MG and NG. ③Only a few apoptotic cells were found at the 7th day in the DG, and more apoptotic cells were found among cardiac muscles at 14th and 21th days. Single apoptotic cardiomyocytes were also found at the outside of the pathological change areas, and no apoptotic cells were found in the animals of NG, MG, and MTG. Conclusions Distinct apoptosis were found in CVB3 viral myocarditis; the activitys of caspase 3 and apoptosis were found at the 7th day, and higher after the 7th day, single apoptotic cardiomyocytes were also found. The high dose Momordicin has distinct inhibitory effect on the activity of caspase 3 and apoptosis.