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Podophyllum hexandrum Royle (Syn. P. emodi Wale) a perennial rhizomatous herb found in alpine region distributed in the entire range of Himalayas from Ladakh to Sikkim at an altitude of 3000-4200 m as1 is an preferred commercial source of Podophyllum lignans. It contains three times more Podophyllotoxin than the American species, Podophyllum peltatum. The present study was aimed to investigate variation of Podophyllum lignans contents based on six marker compounds viz. Podophyllotoxin; Deoxypodophyllotoxin; Picropodophyllotoxin; Podophyllotoxin beta-D-glucopyanoside; Isopicropodophyllone; 4’-Demethyldeoxypodophyllotoxin, beta-D-lucopyanoside, in P. hexandrum population growing at three locations. Further, ontogenetic and morphogenetic variations of Podophyllum lignan contents were studied to investigate dynamics of accumulation of these compounds. Representative collections from three locations viz., Panikhar, Padam and Tangoli located in Trans Himalayan semi-desert region of Zanskar valley were harvested at three stages (dormancy, active growth and maturity). Plants were dissected into root, rhizome and rhizome-buds, dried separately and assayed for Podophyllum lignan contents by high performance liquid chromatography. (C) 2010 Elsevier B.V. All rights reserved.