A reference method (higher accuracy) and a routine method (higher throughput) were developed for the extraction of cyanogenic glycosides from flaxseed. Conditions of (essentially) complete extraction were identified by comparing grinding methods and extraction solvent composition, and optimizing solvent-to-meal ratio, extraction time, and repeat extraction. The reference extraction method consists of sample grinding using a high-speed impact plus sieving mill at 18 000 rpm with a 1.0 mm sieve coupled with triple-pooled extraction in a sonicating water bath (40 degrees C, 30 min) using 75% methanol. The routine method differs by the use of a coffee mill to grind samples and a single extraction. The 70 and 80% methanol solutions were equal and superior to other combinations from 50 to 100% aqueous ethanol or methanol. The extraction efficiencies of the routine method (relative to the reference method) was 87.9 +/- 2.0% SD (linustatin) and 87.6 +/- 1.9% SD (neolinustatin) using four composite samples that were generated from seeds of multiple cultivars over two crop years and locations across Western Canada. Ground flaxseed was stable after storage at room temperature, refrigeration, or freezing for up to 7 days, and frozen for at least 2 weeks but less than 2 months. Extracts were stable for up to 1 week at room temperature and at least 2 weeks when refrigerated or frozen.