The podophyllotoxin content in rhizome and root samples of Podophyllum hexandrum Royle (with leaf morphological variants, that is, 1, 2 and 3L), an endangered perennial herb and a source of highly valued aryltetralin lignan, collected from 17 different populations (2800 to 3600 m asl) spread across Uttarakhand State of Indian Central Himalaya were analyzed by high performance liquid chromatography (HPLC). In general, podophyllotoxin content (on percent dry weight) of both rhizomes and roots varied significantly (p < 0.05) between the morphological variants. The podophyllotoxin content of rhizomes ranged from 0.012 to 5.480%; maximum and minimum levels were recorded in 2L (Kedarnath population) and 3L variants (Ghangria population), respectively. The mean podophyllotoxin content (population-wise) varied significantly (p < 0.05) between different populations; in general, a positive correlation (p < 0.01) was observed between podophyllotoxin content and increase in altitude; population-wise maximum (2.053%) and minimum (0.045%) levels were recorded in Kedarnath and Dayara-1 populations, respectively. The levels in root samples ranged from 0.021 to 5.800%, similar to those in the rhizomes. While maximum amount (5.800%) was estimated in 2L plants from Kedarnath population, minimum (0.021%) level was found in 2L plants from Ghangria population. The mean podophyllotoxin content across morphological variants (population-wise) was significantly (p < 0.05) higher in Kedarnath population (maximum: 2.090%); a positive correlation (p < 0.01) was found between the podophyllotoxin content and increase in altitude. Amongst all the morphological variants analyzed from different areas, 2L plants of Kedarnath population (highest altitude; 3600 m) exhibited maximum podophyllotoxin content, both in the rhizomes and roots. The observed chemo-diversity amongst morphological variants (leaf number) and populations could be used for selecting elites for multiplication and commercial and/or conservation purposes. Key words: Alpine, cultivation, Podophyllum hexandrum, May apple, podophyllotoxin.