Lung cancer is the most common cancer and the leading cause of cancer-related deaths. Panax ginseng has long been used to treat cancer and other diseases worldwide. Most of the pharmacological actions of ginseng are attributed to a variety of ginsenosides, which are often metabolized by intestinal bacteria into more effective forms. In this study, we found that the antiproliferative activity of ginseng was increased after enzymatic processing of ginseng saponin (50% inhibitory concentration, >70 μg/ml). To elucidate the mechanism by which modified ginseng extract (MGX) induced cell death in human lung cancer cells, the gene expression profiles of A549 cells regulated by MGX were assayed using Agilent PrimeView Human Gene Expression Arrays. The expression of 17 genes involved in the regulation of cell signaling, cell metabolism, transport, and cytoskeleton-regulation was up-regulated, whereas the expression of 16 genes implicated in invasion and metastasis and cellular metabolism was down-regulated in MGX-treated A549 cells. Moreover, nuclear staining with 4′,6-diamidino-2-phenylindole revealed that MGX clearly caused nuclear condensation and fragmentation which are observed in apoptosis cell. These results elucidate crucial anticancer mechanisms of MGX and provide potential new targets for the assessment of anticancer activity of MGX.