Quality of pomegranate juice from two Macedonian varieties "Karamustafa" and "Hicaz" was object of this study. Although "Karamustafa" is autochthonous pomegranate variety, morphological and chemical parameters indicated higher quality of freshly squeezed juice for "Hicaz" pomegranate variety. With exception of the amount of organic acid, in particular malic and citric acid and total quantity of catechins, all other chemical parameters were in favor to freshly squeezed juice from "Hicaz" pomegranate variety. Furthermore, the level of the anthocyanins was significantly higher to this pomegranate variety and it was in good correlation to the results of hue and color of the juice. The most statistically significant difference was obtained for ascorbic acid which was four time higher for freshly squeezed juice from "Hicaz" pomegranate variety. In addition, the variation of elemental composition of fruit juices from both variety could be attributed to the difference in cultivar. Finally, the strong antibacterial activity against Staphylococcus aureus (ATCC 25923) was significant without statistical differences between both varieties.