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Polyphenols are important compounds in red wine that determine the color, stability, sensory characteristics, astringency and bitterness as well as stabilizing wine during the aging period. This study is focused on the determination of polyphenols, including flavonoids (anthocyanins, pyranoanthocyanins, flavonols and flavan-3-ols) and non-flavonoids (phenolic acids and stilbenes), in red Kratošija wines, applying HPLC-ESI-MS/MS method. The wines were produced using two commercial yeasts for fermentation in order to study the effect of the yeast on the phenolic compounds profile and content. The chromatographic separation of compounds was performed by using a mobile phase consisting of acetonitrile as solvent A and formic acid (pH 2.8) as solvent B, in a gradient mode, as follows: 0-3 min 10% A, 3-10 min 20% A, 10-15 min 25% A, 15-31 min 90% A and 31-50 min 100% A. Wine samples were injected directly into the HPLC system, after filtration through 0.20 μm polyester membrane, using Kinetex C18 column (100 x 2.1 mm, 2.6 µm) for separation. The accuracy and precision of the method were evaluated and the LOD, LOQ and correlation coefficient were determined. The method showed satisfactory characteristics for the analysis of phenolic compounds in red wine. In the wine samples, analytes were identified based on the knowledge of their fragmentation pathway and by comparing the retention times with their reference standards. Quantification was performed by constructing calibration curves for the available standards and for the other compounds, relative amount was calculated based on the peak area calculation from the appropriate ion peak chromatogram. It was found that the content of polyphenolic compounds was significantly influenced by the yeast strain suggesting that the phenolic profile of wine can be modulated through the appropriate selection of yeast for fermentation.