Flaxseed and its major mammalian lignan precursor secoisolariciresinol diglycoside have been shown to be protective against chemically induced carcinogenesis in animal models. Although flaxseed is the richest source of mammalian lignan precursors, it is not known whether these levels vary with source. Thus the objective of this study was to determine how lignan levels in flaxseed are affected by variety, growing location, harvest year, and seeding time. Ten varieties of flaxseed (AC Linora, Andro, Flanders, Linott, McGregor, Noralta, NorLin, NorMan, Somme, and Vimy) were subjected to 1) in vitro fermentation with human fecal inoculum for 24 hours under anaerobic conditions to assess mammalian lignan production and 2) high-performance liquid chromatography (HPLC) analysis for secoisolariciresinol levels. Three of these varieties (Linott, McGregor, and NorLin) were grown in four locations, seeded early (May) for three different years, and, in one year, seeded early (May) or late (June). Significant differences in lignan production were observed among the different varieties, ranging from 0.96 mumol/g for Linott to 3.15 mumol/g for Somme flaxseed (p < 0.05). Growing location had significant effects on lignan production from all three varieties. Harvest year significantly affected only the Linott variety (p < 0.05), whereas seeding time had no effect. A significant correlation (r = 0.572, p < 0.003) was observed between lignan values obtained from HPLC and in vitro fermentation methods, indicating that HPLC analysis of flaxseed may be used as a predictor of its lignan production levels. Differences due to variety, harvest location, and harvest year of flaxseed should be taken into consideration when tumorigenesis studies are designed.