This is the first study to analyse the profiles of anthocyanin (ACN) and organic acid (OA) and some physico-chemical properties of pomegranate juices (PJs) obtained from nine registered varieties in Turkey. HPLC analyses revealed that there were significant differences between ACN contents (28–447 mg L−1) and profiles (P < 0.01). The PJs contain maximum six ACNs, 3-glucosides and 3,5-diglucoside of delphinidin, cyanidin and pelargonidin. The major OA in PJs was citric acid (66–74%), followed by malic (6–12%), succinic (5–19%), nonidentified (0–14%) and tartaric acids (0.1–3.7%). Amongst individual OAs, citric acid had the most significant effects on TA (r = 0.9761), pH (r = 0.9208) values and sourness of PJs. As different from literature, results of this study revealed that malic acid contents of authentic PJs could be higher than 1.5 g L−1. Consequently, ACN and OA profiles could be successfully used in quality control because all PJs have their own typical ACN and OA profiles.