Plant lignans are natural products resulting from the phenylpropanoid metabolic pathway. Lignans are of considerable interest in the treatment of cancer and other diseases. After a survey on plants containing lignan, Jatropha Gossypifolia (J.G) with lignan Arylnaphthalene was selected, which showed structural similarity with synthesized lignan (1-phenylnaphthalene). Plant Jatropha Gossypifolia has potent anticancer activity, have already been proved by various researchers. In a follow-up study, the lignans synthesized in our laboratory were also tested for its invitro cytotoxic activity using MTT assay. The results were found to be significant. A simple, rapid and specific method for the analysis of structurally similar lignan in the plant Jatropha Gossypifolia with synthetic organic compound (1-phenylnaphthalene) by a sensitive High Performance Liquid Chromatography technique is developed. The lignan peak was separated from endogenous peaks on phenomenex ODS 5μ C18 column (250 x 4.6mm) with mobile phase comprising of phosphate buffer: acetonitrile (70:30), pH-2 at a flow rate of 1ml/min and Ultra Violet detector at 230nm. Lignan 1-phenylnaphthalene was eluted at 4.047 minute and lignan from plant J.G was eluted at 4.077 minute.