The aim of this study was to evaluate the effect of rye flour extraction rate on the protein amino acids content and protein quality indexes (chemical score, CS, protein efficiency ratio, PER) of traditional rye bread and ginger cake and to compare them with conventional wheat bread. Rye flour with extraction rates of 1000 g/kg and 920 g/kg (F-1000 and F-920, respectively), were used. Amino acid content was determined by HPLC and protein quality indexes were calculated. The results showed that contents of non-essential amino acids (NEAA) were not much affected by flour extraction rate in rye bread and ginger cake since only Asp and Ser were higher in F-1000 rye bread and Arg and Pro in F-1000 ginger cake. In regard to essential amino acids (EAA), only Thr and Val content was significantly higher (P≤0.05) in F-1000 rye bread, on dry weight basis. In addition, rye bread formulated with whole rye flour exhibited a higher content of total EAA than wheat bread (P≤0.05). Regarding protein quality indexes, CS values were quite low in breads and ginger cakes, being Lys the limiting amino acid. However, estimated PER values were similar among wheat and rye breads, and slightly lower for ginger cakes. Hence, whole rye flour should be considered as an approach to improve the nutritional quality of traditional rye-based products.