The relative influences of parent lithology and anthropogenic effects on the soil geochemistry of Cyprus have been evaluated using a high density soil survey. Cyprus contains a number of lithologically distinct terranes, including the ultramafic–mafic Troodos Ophiolite Complex, which hosts a number of Cyprus-type Cu deposits, and the surrounding carbonate-rich marine sedimentary units. Cyprus also has a long history of human settlement and resource exploitation. Top-soils (0–25 cm depth) and sub-soils (50–75 cm) were grid-sampled across the southern two-thirds of the island at a density of 1 site per c. 1 km2. The aqua regia-extractable and total element contents of the <2-mm fraction were determined using a range of analytical techniques. For most elements the soil geochemistry is dominated by parent lithology and subsequent regolith processes. Major urban areas, industrial zones, Cu mines and some other locations display elevated contents of Pb, Cu, Hg, Sn and Zn, especially in top-soil. The northern Polis Valley displays elevated Hg in sub-soil which appears unrelated to either geological features or modern anthropogenic influences. Contaminated areas are typified by significant differences between top-soil and sub-soil element concentrations as well as changes in multivariate geochemical patterns.