The MTT assay, as a screening method, has been widely used to measure the viability and proliferation of cells. However, it should be noted that MTT assay may not accurately reflect the effect of Cistanche tubulosa ethanolic extract on EA.hy926 cells viability. To investigate and identity the components responsible for the contradictory observations of the MTT assay, echinacoside and acteoside, two main phenylethanoid glycosides, from C. tubulosa ethanolic extract were isolated. The data derived from CCK-8, Hoechst 33342 and annexin V-FITC/PI assays suggest that the caffeyl group present in both isolated compounds was responsible for the conflicting results of the MTT assay. These data emphasize the need of using a variety of different methods to determine the effect of medicinal agents on cell viability to avoid generating misleading results.