Current food industry practices include the use of pasteurization (heat treatment) as a means to reduce the microbial counts of flaxseed (Linum usitatissimum). Flaxseed was pasteurized using a dry air heat treatment of 148 °C for 16.25 minutes and the oxidative stability was observed over a 20 week storage period. Flaxseed quality was measured using peroxide value, percent free fatty acid (as oleic), and propanal content. Peroxide values of the pasteurized milled flaxseed were found to significantly increase (P ≤ 0.05) by week 2. Propanal formation coincided with peroxide value development over 20 weeks of storage. Pasteurized flaxseed milled under refrigerated temperatures (10 – 18 °C) did not exhibit any significant (P > 0.05) improvement in oxidative stability. Flaxseed pasteurization at 148 °C for 16.25 minutes using dry heat was found to be detrimental to the oxidative stability flaxseed once milled.