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Galium sinaicum is a wild medicinal plant in saint Catherine, Egypt. To distinguish apoptotic effect of G. sinaicum ethanol extract (GsEE), we examined the role of GsEE in inducing programmed cell death (PCD) of Allium cepa root meristematic cell (AcR). Cells was subjected to GsEE in definite concentrations (0.1,0.3, 0.5%) and duration (6, 12h), then PCD induction was assessed. Application of GsEE arrested the mitotic division of AcR with metaphase accumulation. Electron microscopy analysis demonstrated ultrastructural alterations of organelles verifying PCD hallmarks. Protein electrophoresis analysis of AcR revealed a change in protein profile of Allium cepa root, also quantitative analysis showed significant increase in nuclease activity enzymes that stimulated DNA laddering fragmentation. Additionally, cell proliferation of MCF-7 and BHK21 was arrested by GsEE. Apoptotic effect of G. sinaicum may be attributed to the presence of potent phenolic compounds such as querectin and rutin as established by HPLC phenolic fingerprint analysis.