A highly sensitive ultra-performance liquid chromatography coupled with triple quadruple mass spectrometry (UPLC-TQ-MS) was applied for simultaneous determination of seven biogenic amines (cadaverine, putrescine, histamine, spermine, tyramine, phenyethylamine and tryptamine) in Montenegrin red Vranac and Kratošija (Vitis Vinifera L.) wines. The method was validated, confirmed the suitability for determination of biogenic amines in red wines and was applied to examine the changes of biogenic amines in three vinification stages: after alcoholic fermentation, malolactic fermentataion and ten months of aging of the wines. The results showed that the total amine levels were low, ranging from 1.27 to 3.26 mg/L, observing increased concentration in the wines after finished malolactic fermentation. Putrescine, which was constituted as a main amine in wines (range: 0.79 to 2.39 mg/L), was observed in a slightly higher content in Vranac wines compared to Kratošija, followed by the aliphatic cadaverine (range: 0.091 to 0.35 mg/L) and the aromatic phenylethylamine (range: 0.119–0.373 mg/L). Histamine and tyramine which are subject of toxicological interest, were present in a very low concentration in wines (on average value: 0.082 and 0.015 mg/L, respectively). Cadaverine and putrescine significantly correlated with the sum of total biogenic amines, even the reached values were below the toxicity threshold. According to the principal component analysis, wines were clearly separated in three groups according to the three vinification stages.