A method for the characterization and quantitation of phyto-estrogenic lignans from pomegranate (Punica granatum L.) fruits and fruit-derived products by HPLC-DAD-MS(n) was developed. For this purpose, edible and nonedible parts of pomegranate (aril, peel, mesocarp, seed, and twigs), commercial juices, juices produced on pilot-plant scale, and encapsulated dietary supplements were analyzed. In addition to the peel, mesocarp, and twigs, lignans were detected in two juices obtained from entire fruits, four commercial juices, and three encapsulated pomegranate extracts. Isolariciresinol was the predominant lignan with contents of 5.0, 10.5, and 45.8 mg/kg dry matter in processed pomegranate mesocarp, peel, and twigs, respectively. In contrast, due to their low amounts, quantitation of lignans in pomegranate products was impossible. Therefore, contrary to previous assumptions, lignans were found to be less relevant in pomegranate-derived products. However, the byproduct from pomegranate processing may be used for lignan extraction. The method presented allows one to differentiate between pomegranate-derived products obtained from fruits without peels or by dejuicing applying low pressures, which were devoid of lignans, and those obtained from entire fruits applying high pressures, thus containing lignans. Consequently, this study helps to optimize process technology aiming at the recovery of preparations with well-desired compositions, which may reduce the risk of a wide range of diseases, such as certain types of cancer.