The phenolic composition of Malbec (Vitis vinifera L.) grape skins and seeds during ripening and the effect of cluster thinning (CT) in two consecutive seasons (2008-2009) were evaluated by high-performance liquid chromatography-diode array detection/electrospray ionization-mass spectrometry (HPLC-DAD/ESI-MS). Removal of 50% of clusters was performed at 40 days (T1), 80 days (T2), and 100 days after flowering (T3) in a vineyard located in southern Mendoza (Argentina). Yield components, with the exception of cluster weight, were significantly affected by CT in both seasons, but no statistically significant differences were found among treatments. Cluster thinning and its timing had little or no influence on physical parameters and fruit chemical composition, and the differences with respect to the control were mainly due to the season. At harvest in 2008, T1 encouraged the biosynthesis of individual anthocyanins in skins, generating 44.0, 39.6, and 41.2% more glucosylated, acetylated, and total anthocyanins, respectively, as compared to the control, whereas in seeds, T1 and T2 mainly changed the concentrations of (+)-catechin, epicatechin-3-gallate, procyanidin B4, dimer gallate 1, trimer gallate 2, and tetramer. Conversely in 2009, T1 significantly affected the content of flavanols and flavonols in skins, whereas in seeds, T1 and T2 modified the level of (+)-catechin, procyanidins B4 and B6, and trimer gallate 2. Moreover, in 2008 the grapes had a higher concentration of most phenolic compounds, indicating a greater potential for more complex wines. Finally, dihydroquercetin-3-glucoside was the major compound among all nonanthocyanin phenolics detected in Malbec skins and represented 25.7% (2008) and 39.9% (2009) of the total content of those compounds at harvest. This finding could represent a distinctive feature of this grape variety.