Objectives: We aim to exploring the association among the gene polymorphisms of multidrug resistance gene 1 (MDR1) and cytochrome P450 3A4 (CYP3A4), the blood concentration of mifepristone and the outcomes of mifepristone in medicine abortion, in order to developing an individualized treatment of mifepristone. Methods: 126 patients of medicine abortion were enrolled, which received a regimen of mifepristone and misoprostol. The blood concentration of mifepristone and monodemethyl-mifepristone was detected by LC-MS/MS analysis. Polymorphisms of MDR1 3435C>T, 1236C>T, 2677G>T/A and CYP3A4*1G were genotyped by MassARRAY technology. Results: The patients in successful outcome group have a higher blood concentration of both mifepristone and monodemethyl-mifepristone than that in failed outcome patients (P = 0.031 and 0.012, respectively). Meanwhile, there was a relationship between the C/D ratio of mifepristone, monodemethyl-mifepristone and the efficacy of mifepristone (P = 0.040 and 0.017, respectively). In addition, the occurrence of adverse reaction of mifepristone was associated with a higher blood concentration of mifepristone as well as C/D ratio of mifepristone (P = 0.010 and 0.008, respectively). MDR1 G2677T/A was linked with the C/D ratio of mifepristone and monodemethyl-mifepristone (P = 0.012 and 0.004, respectively), as well as the efficacy and adverse reaction of mifepristone (P = 0.042 and 0.001, respectively). CYP3A4*1G genotype was related with a lower blood concentration of mifepristone (P = 0.012). Conclusion: The blood concentration of mifepristone and monodemethyl-mifepristone and MDR1 2677G>T/A could be a reliable indicator in a successful outcome of mifepristone for medicine abortion and the occurrence of adverse reaction.