This article contains data on in vitro cytotoxicity activity of chloroform, methanolic and water extracts of leaf and heartwood of Caesalpinia sappan L. a medicinal plant against Breast cancer (MCF-7) and Lung cancer (A-549) cells. This data shows that Brazilin A, a natural bioactive compound in heartwood of Caesalpinia sappan L.induced cell death in breast cancer (MCF-7) cells. The therapeutic property was further proved by docking the Brazilin A molecule against BCL-2 protein (an apoptotic inhibitor) using auto dock tools. Keywords: Chloroform extract, Methanol extract, Water extract, Caesalpinia sappan L., Cytotoxicity, MCF7, A549, MTT Assay