Objective To investigate the effect of low dose low molecular weight heparin (LMWH) on acute pancreatitis (AP). Methods 98 AP patients who were admitted in our hospital from 2002 to 2008 were randomly divided into anticoagulant therapy group (n = 40) and control group (n = 58). Anticoagulant therapy group consisted of 15 cases of severe acute pancreatitis (SAP) and 25 cases of mild acute pancreatitis (MAP) ; while there were 19 cases of SAP and 39 cases of MAP in control group. The patients of control group received conventional treatment, and conventional therapy together with 3 000 U LMWH subcutaneous injection every 12 hours were used in anticoagulant therapy group for two weeks. The changes of APACHE II score, complication rate, mortality and length of hospital stay were observed and the coagulation changes before and after anticoagulant therapy were documented. Results 7 days later, the APACHE II score, complication rate, mortality and length of hospital stay of SAP patients in the anticoagulant therapy group were 9. 9 ±4. 9, 20% , 13.3% , (20.6 ±10.4)d, respectively; while they were 12. 2 ±4.8, 42. 1%, 47.4%, (28. 2 ± 12. 5) d, respectively, in the control group, and the difference was statistically significant (P < 0. 05). The corresponding values were not statistically significantly different among MAP patients in the two groups. The coagulation after treatment in anticoagulant therapy group was not statistically different with that before treatment. Conclusions Low dose LMWH could reduce the rate of complication rate, mortality and decrease the length of hospital stay, without complication of hemorrhage, which should be recommended in the early phase of SAP.