This study examined the stability of whole and ground flaxseed, either alone or as an ingredient in a muffin mix, by measuring oxygen consumption and changes in α-linolenic acid under various conditions. When ground flaxseed was heated at 178°C in a sealed tube, headspace oxygen decreased from 21 to 2% within 30 min, while that of whole flaxseed decreased only slightly up to 90 min at 178°C. Under the same conditions, the oxygen consumption of lipids extracted from an equivalent amount of flaxseed was between the whole flaxseed and the ground flaxseed. After heating to 178°C for 1.5 h, α-linolenic acid decreased from 55.1 to 51.3% in ground flaxseed, and to 51.7% in lipid extracts, but it remained unchanged in the whole flaxseed. Ground flaxseed with large (<20 mesh) or small (>35 mesh) particle size absorbed more oxygen than samples with medium particle size when heated at 122°C for 8 h. Long-term storage of whole or ground flaxseed or lipid extracts showed that all three preparations were stable at room temperature for 280 d with 12 h light/dark cycles. A muffin mix, containing 28.5 wt% flaxseed flour, consumed oxygen more rapidly than a control muffin without flaxseed flour at a baking temperature of 178°C for 2 h, but the α-linolenic acid remained unchanged in both muffin mixes. Polymers derived from triglyceride oxidation and newtrans isomers of α-linolenic acid were not detected under the present experimental conditions. Under typical baking conditions, there is minimal loss of α-linolenic acid from flaxseed, although the manner of incorporation of flaxseed in food products should be considered to minimize oxidation of α-linolenic acids.