The stable isotope ratios ((13)C/(12)C and (15)N/(14)N) of casein measured by isotope ratio mass spectrometry (IRMS) and some free amino acid ratios (His/Pro, Ile/Pro, Met/Pro, and Thr/Pro) determined by HPLC in samples of ewes' milk cheese from Sardinia, Sicily, and Apulia were found to be parameters independent of ripening time. Multivariate data treatments performed by applying both unsupervised (principal component analysis and cluster analysis) and supervised [linear discriminant analysis (LDA)] methods revealed good discrimination possibilities for the cheeses according to place of origin. In this respect, particularly significant were the variables Ile/Pro, Thr/Pro, (13)C/(12)C, and (15) N/(14)N ratios on which basis 100% discrimination and classification of the samples by LDA was obtained.