The phenolic composition of grape pomace seeds and skins in the South Tyrolean autochthonous variety Lagrein has been studied for three different microfermentation experiments. 23 anthocyanins and 9 flavan-3-ols were determined by UHPLC-MS/MS in both the skins and seeds of grapes and pomace. The remaining contents of total polyphenols, total anthocyanins and the antioxidant capacity of the pomace after maceration, as measured by the DPPH, FRAP and ABTS methodologies, depended not only on the initial contents in the grapes, but also on the maceration time. Even though all anthocyanins in skins were highly reduced during the maceration (maximum recoveries of 40%), the residual contents in the pomace were still considerable (2-8 mg/g fresh weight, FW). The content of flavan-3-ols in seeds remained very stable (recoveries of 70-100%). Our results show that the Lagrein grape pomace is a promising source for antioxidant phenolic compounds that can be of interest as nutraceuticals.