Pistachio (Pistacia vera L.) belongs to the Anacardiaceae family and it is a small tree species. It is native of the Middle East and Central Asia, but currently, it is cultivated also in California and in some Mediterranean countries, such as Greece and Italy. The most important pistachio producers are Iran, the USA, and Turkey. Besides being a delicious nut, pistachio, due to its wholesome nutritional properties, could be considered as a functional food. According to the results of several studies, pistachios have been proven to have various groups of valuable phytochemicals such as anthocyanins, flavan-3-ols, proanthocyanidins, flavonols, isoflavones, flavanones, stilbenes, and phenolic acids, possessing excellent biological activities. The most common analytical technique employed for their analysis is represented by liquid chromatography coupled to photodiode array and mass spectrometry detection. However, conventional LC can present some limits especially in terms of resolving power. In this contribution, as a powerful alternative, comprehensive two-dimensional liquid chromatography (LC×LC) was applied to the determination of the polyphenolic fraction of pistachio kernels from different geographical origins. A 150-mm micro-bore cyano column (2.7μm dp) and 50-mm superficially porous C18 silica column (2.7μm dp) in the first (1D) and second (2D) dimensions were employed, respectively. For boosting orthogonality, a shift 2D gradient was investigated leading to an increase in the overall peak capacity. The newly developed LC×LC method showed satisfactory linearity, sensitivity, precision and accuracy, which was then applied to sample quantitative analysis. A total of 51 different polyphenolic compounds were determined in the four samples investigated and 18 out of them are hereby reported for the first time.