The laterite deposits (Fe–Ni-laterite and bauxites) in the Balkan Peninsula are mainly located in the Mirdita–Sub-Pelagonian and Pelagonian geotectonic zones and are of great economic significance. These deposits have been affected by intense tectonism, which has created overthrusting, foliation, folding, and faulting. The investigation of arsenic in laterites is thought to be important for the ferronickel smelting process and the serious affect of the health. Minerals such as iron oxides and pyrite are of particular significance in controlling arsenic mobility, and hence aquifer contamination. Laterite samples from Ni-laterite deposits of Greece (Lokris, Vermio, Edessa, Olympos, Kastoria), Albania (Bitinca and Gouri-Perjuegjiun), Serbia (Rzanovo and Topola), bauxitic laterites and the Parnassos-Ghiona bauxite deposit were analyzed for major and trace elements, including arsenic (As). Arsenic concentrations for all laterite samples from the Balkan Peninsula range from < 2 ppm to a few decades ppm. However, arsenic concentrations for the individual laterite occurrences and deposits from Aghios Ioannis vary significantly from <2 ppm to 2600 ppm. Arsenic in the Parnassos-Ghiona deposit ranges from <10 ppm in typical red colored ore to 900 ppm in yellow-grey colored ore. The latter type occurs along and near faults and constitutes a significant (approximately 30 vol. %) portion of the bauxite ores. They are characterized by the presence of abundant pyrite and micro-organisms. Elevated arsenic contents are mostly associated with Fe-oxides/hydroxides in Ni-laterites, showing enrichment in REE, Co, Ni, Th and U contents, and with Al-oxides in bauxites. The sulphur isotope compositions of Fe sulphides from the bauxite deposit show a range from +10.2 to –30.2 per mil. Most negative values were obtained from grey-coloured ore samples. The organic matter may be related to the source of arsenic and play a major role in controlling the redox conditions, since they can drive the formation of pyrite or Fe-oxides.