In vitro studies show the antioxidant potential of flaxseed protein hydrolysates. In this work it was studied by principal component analysis (PCA), the correlation between degree of hydrolysis (DH) and antioxidant capacity (AC) of the hydrolysates, and the distinction between the deffated flaxseed meal, protein concentrate and hydrolysate in relation to the mechanism of antioxidant capacity in different extracts. Flaxseed protein isolate (FPI) was obtained from defatted flaxseed meal (DFM) and the protein hydrolysates (FPH) were obtained from hydrolysis of the FPI with Alcalase in a two factor central composite rotatable design (pH 7.5 to 9.5 and enzyme:substrate ratio 1:150 to 1:90, w/w). The hydrolysates were characterized by DH using the pH–Stat procedure. In aqueous and methanolic (70%) extracts of hydrolysates were evaluated total phenolic content (TFC), by Folin-Ciocalteau and AC by ORAC and FRAP methods. Data were autoscaled and for PCA was used the software Pirouette 3.11. The correlation between DH and AC were determined using three principal components (84.04% of explanation) and the extraction in methanol was the strongest influence on the AC and TFC. To distinguish the samples (DFM, FPI and FPH) were used two principal components (97.73% of explanation) and the highest influence was the AC measured by ORAC in aqueous extract. The results suggest that ORAC method is that best distinguishes the AC of the samples. Among the hydrolysates, the compounds in methanol extracts, with higher hydrophobic character, are the most relevant in the characterization of AC.