Limited data on the behavior of impurity elements during the formation of ore minerals in hydrothermal systems reduce their potential as indicators of the physicochemical conditions of ore formation. One of the most common sulfides capable of concentrating precious metals and other valuable components is pyrite. The distribution of a number of typomorphic impurity elements in pyrite under its crystallization in hydrothermal conditions at a temperature of 450 °C and a pressure of 1 kbar was studied. Using X-ray spectral microanalysis, scanning electron microscopy, and inductively coupled plasma and laser ablation mass spectrometry, data were obtained on the forms of occurrence, content ratios, and correlation relationships of impurity elements in the volume and surface layer of pyrite crystals. For the first time, the parameter S of surface phase selectivity with respect to main (Co, Cu, Ni) and minor impurities (noble metals, As, Zn, Mn) was determined, which averaged 1.9 (Co), 2.1 (Cu), 1.3 (Ni), 4.2 (Pd), 18.5 (Au), 6 (As), 10.2 (Zn), and 9.1 (Mn). The correlations between elements are significantly different for the surface and volume, which is explained by the influence of surface phase selectivity. The dual nature of the correlation between Au and As allows their relationship to be considered a surface phenomenon. Palladium, a critically important metal widely used in chemical catalysis and other areas of technology, exhibits unusual behavior in pyrite, concentrating mainly on its surface, which suggests the possibility of its concurrent extraction from pyrite ores at gold extraction enterprises. The observed correlations are considered from the perspective of the incorporation of impurity elements into the bulk structure of pyrite and into the compositions of surface phase-like formations (non-autonomous phases) that evolve during crystal growth and are enriched with incompatible elements.