Soybean isoflavone genistein has multiple anticancer properties and its pro-apoptotic and anti-proliferative effects have been studied in different cancer cells. However, the mechanisms of action of genistein and its molecular targets on human colon cells have not been fully elucidated. Therefore, caspase-3 and p38 mitogen-activated protein kinase (p38 MAPK) as the main therapeutic targets were investigated in this study at both gene expression and protein levels in HT29 colon cancer cells. The caspase-3 and p38 MAPK gene expression levels were examined by real time PCR whereas flow cytometry technique was performed to determine their intracellular protein levels. The caspase-3 enzyme activity was obtained by colorimetric method while the gelatinase activity of matrix metalloproteinase-2 (MMP2) was determined by zymography. In addition, MTT test, wound healing assay and clonogenic assay were carried out to determine the effect of genistein on HT29 cell viability, migration, and proliferation, respectively. Genistein induced apoptotic death in HT29 cells through activation of caspase-3 pathway at the transcriptional, protein, and enzymatic levels. Moreover, genistein inhibited the proliferation of HT29 cells by reducing of both p38 MAPK gene expression and its active phosphorylated protein level. Also, we showed that genistein strongly suppressed the metastatic potency of HT29 colon cancer cells via the reduction of MMP2 activity. Based on the results of this study, we conclude that genistein may exhibit its anticancer properties on HT29 colon cancer cells by modulating caspase-3 and p38 MAPK pathway at different transcriptional and protein levels.