The free amino acid patterns of unfermented and fermented wheat sour doughs started with Lactobacillus plantarum were related by factor analysis to dough yield, ash content of flour, fermentation temperature and presence/absence of yeast, from data corresponding to a central composite design of samples. Individual levels of hydrophobic, acid and basic amino acids as well as total amino acid content positively correlated with extraction rate of flours. The presence of yeast promoted metabolism of histidine, aspartic acid and asparagine, particularly in samples made with whole and wholemeal flours. Proliferation of predominant amino acids by enzymatic release was more notable at higher fermentation temperatures and wholemeal samples. Sour doughs with maximum levels of hydrophobic and basic amino acids were started with no yeast bacterial cultures, made with whole and wholemeal flours and fermented at 35°C.