Three extraction methods for analysis of podophyllotoxin and its derivatives from Linum species were compared. No statistical difference on the percentage of recovery were found between the methods. The "glycosidase-method" showed the best result with respect to the accuracy studies; the "acetone-method" has an advantage compared to the other methods due to its capability to calculate the aglycone, lignan glycoside and total lignan. The content of podophyllotoxin and 6-methoxypodophyllotoxin in Linum mucronatum subsp. mucronatum Bertol, Linum arboreum L., and the endemic Turkey species of Linum flavum subsp. scabrinerve Davis were determined. This is the first report on the analysis of podophyllotoxin and 6-methoxy podophyllotoxin of natural collected Linum flavum subsp. scabrinerve and Linum arboreum.