Abstract Thermal characteristics of ion-exchange protein fractions from dehulled delipidated meal of four flaxseed cultivars grown at three locations were evaluated by differential scanning calorimetry (DSC) to examine genotypic and environmental effects. DSC was performed in a “dry” state on four, 0.28, 0.35, 0.45 and 0.50 M NaCl lyophilized protein fractions. Flaxseed proteins exhibited two thermal events between 83 and 115 °C with distinct shoulders present in the 0.45 and 0.50 M fractions of all cultivars. Cultivar and location effects were significant for the first thermal transition ( T d 1 ) of the 0.28 and 0.35 M fractions, and the second transition ( T d 2 ) of the 0.35, 0.45 and 0.50 M fractions. The enthalpy of the first transition Δ H 1 of the 0.35 and 0.50 M fractions was cultivar dependent, while that of the second transition Δ H 2 was cultivar and location specific for the 0.35, 0.45 and 0.50 M fractions. The 0.28 and 0.45 M fractions displayed the lowest and highest thermal transition temperatures, respectively. All protein fractions consisted of reversing and nonreversing thermal events as assessed by modulated DSC. Flaxseed cultivars, when grouped by thermal characteristics of protein fractions, can be differentiated by principal component analysis.