We studied vertical changes in the chemical composition of zircon from two contrasting Variscan granite systems. The Beauvoir system (Massif Central, France) composed of three successive intrusions (B1, B2, B3) represents typical peraluminous S-type granite extremely enriched in P, F, Li, Rb, Cs, Be, Sn, Nb, Ta, and poor in Zr, Th, REE and Y. The Cinovec system (Krusne hory Mts/Erzgebirge, Czech Republic/Germany) composed of two successive intrusions (protolithionite granite, zinnwaldite granite) is only slightly peraluminous, P-poor, F, Li, Rb, Cs, U, Th, REE, Y, Sc, Sn, W, Nb, Ta-rich granite, which may be classified as A-type. In both localities, the most fractionated intrusions are located on the top of the system. Samples from borehole GPF-1 (Beauvoir) represent an 800 m long vertical section through the entire granite stock, while CS-1 borehole (Cinovec) reached a depth of 1600 m. Chemical compositions of zircons from both granite systems show distinct vertical zonality, but their shape and elemental speciation is highly contrasting. At Beauvoir, zircon shows a remarkable increase in Hf-content from 2–4 wt. % HfO₂ (~0.03 apfu Hf) in the deepest B3-unit to 15–19 wt. % HfO₂ (up to 0.18 apfu Hf) in the uppermost B1-unit. The highest contents of F, P, and U were detected in the intermediate unit B2 at a depth of 400–600 m. At Cinovec, Hf shows only moderate enrichment from ca. 2 wt. % HfO₂ in the deeper protolithionite granite to 5–10 wt. % HfO₂ in the uppermost part of the zinnwaldite granite. High contents of Th (3–8 wt. % ThO₂) are entirely bound in the uppermost section of the granite copula to a depth of 200 m, but below this level the contents only sporadically exceed 1 wt. % ThO₂. Concentrations of U, Y, HREE, Sc and Bi also reach their highest values in the uppermost parts of the zinnwaldite granite, but their decrease downward is much gentler. Extreme enrichment of outer zones of zircon crystals from some granites with Hf or high contents of Th, U, REE, Y, Nb and of some other elements in zircons from other localities is not considered to be a specific phenomenon characterizing melts of A- or S-type granite, but reflects a high degree of fractionation of systems rich in Na and F.