Pistachios are a nutritionally beneficial food source widely consumed all over the world. Pistachios exhibit high content of antioxidants, vitamins and other beneficial micronutrients, including nutrient elements and rare earth elements (REEs). Considering that the concentration of REEs depends on the climate and soil characteristics that vary among different geographical regions, REEs could constitute markers responsible for the geographical discrimination of this nut type. In this study, Greek pistachios with a protected designation of origin (PDO) label from Aegina Island and Fthiotida and Turkish pistachios from Adana were analyzed with inductively coupled plasma mass spectrometry (ICP-MS) to assess their REE profile. La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm and Yb were determined and quantified. The quantification results were further analyzed using the main effect plot, permutational analysis of variance (PERMANOVA), nonmetric multidimensional scaling (nMDS), principal component analysis (PCA) and hierarchical clustering (HCA) to investigate the similarities between the pistachios. A decision tree (DT) was developed for the classification of pistachios according to their geographical origin proving to be a promising and reliable tool for verifying the authenticity of food products on the basis of their REE profile.