The physical and chemical properties of twelve cultivars of pomegranate (Punica granatum L.) grown in different regions of Iran were investigated by multivariate analysis method. The fruit fresh weight and volume, fruit density, fruit neck diameter, fruit peel weight, fruit peel percent, fruit aril percent, juice content, peel thickness, seed percent, total soluble solids, titrable acidity, harvest index, reducing sugars, pH, electric conductivity (EC), vitamin C, ellagic acid and tannin content of juice and peel (using HPLC) and total antioxidant activity of juice and peel (using FRAP assay) were the measured characters. Results showed a considerable variation in the studied properties. Cases of homonymy existing among cultivars were shown as cluster analysis. Based on the principal component analysis among measured parameters a big variability was observed. The first component correlated positively with fruit density, seed percent, titrable acidity, ellagic acid content of peel, and negatively with fruit fresh weight and volume, fruit peel weight, fruit aril percent, aril juice percent and fruit density. The second component had positive correlation with harvest index, pH, reducing sugars, ellagic acid content of juice, ellagic acid content of peel and negative correlation with fruit density, total acidity, electric conductivity and fruit peel thickness. Discrimination analysis classified 98% of specimens to correctly expected groups. Most effective characters in discrimination were fruit aril percent and volume with positive correlation, pH, and ellagic acid content ofjuice with negative correlation to first extracted function. Second extracted function showed positive correlation with ellagic acid content of peel, fruit fresh weight, harvest index and negative correlation with fruit peel weight, aril juice percent and fruit peel thickness.