Microcystins (MCs) are a family of cyclic heptapeptide hepatotoxins produced by freshwater species of cyanobacteria which have been implicated in the development of liver cancer, necrosis and even deadly intrahepatic bleeding. Microcystin-LR (MC-LR), the most toxic MC variant, is also the most commonly encountered in a contaminated aquatic system. This study presents the first data in the toxicological research of MCs which combines the use of standard apoptotic assays with transcriptomics, proteomics technologies and computer simulations. By using histochemistry, DNA fragment assays and flow cytometry analysis, we determined that MC-LR causes rapid, dose-dependent apoptosis in mouse liver when BALB/c mice are treated with MC-LR for 24 hours at doses of either 50, 60 or 70 mg/kg body weight. We then used gene expression profiling to demonstrate differential expressions (>2-fold) of 61 apoptosis-related genes in cells treated with MC-LR. Further proteomic analysis identified a total of 383 proteins, of which 35 proteins were up-regulated and 30 proteins were down-regulated more than 2.5-fold when compared with controls. Combining computer simulations with the transcriptomic and proteomic data, we found that low doses (50 mg/kg) of MC-LR lead to apoptosis primarily through the Bid-Bax-Bcl-2 pathway, whereas high doses of MC-LR (70 mg/kg) caused apoptosis via an ROS pathway. These results indicated that MC-LR exposure can cause apoptosis in mouse liver and revealed two independent pathways playing a major regulatory role in MC-LR-induced apoptosis, thereby contributing to a better understanding of the hepatotoxicity and the tumor-promoting mechanisms of MCs.