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Powdered plant coagulant obtained from the cardoon flowers (Cynara cardunculus) was compared with calf rennet for the manufacture of traditional raw goats' milk cheese, by determining differences in the profiles of the amino acids throughout the ripening period. Derivatisation with o-phtaldialdehyde and a C 18 column were used for chromatographic separations. In order to establish the relationships between the different variables and to detect the most important causes of variability, principal component analysis was applied to the free amino acids data, which reduced to two dimensions where cheese samples from 2 to 60 days and cheeses from 90 to 120 days were distributed dependently of ripening time and coagulant used. Leu, Val, Lys, Gly, Tyr and Asp were correlated with PC1, which separated the samples according to their ripening time. Arg, His, Trp, Ser and Thr were correlated with PC2, which separated the samples according to the coagulant used.