To examine the suitability of benthic foraminifera and their test deformations as bioindicators of pollution in coastal marine environments, we studied foraminifera and metal concentrations in 72 marine sediment samples, collected from the inner shelf along the Sicilian coast (Gulfs of Palermo and Termini) and on the south-eastern coast of Lampedusa Island. These areas are characterised by different environmental conditions. On the basis of pollution sources and foraminiferal assemblages, we recognised different zones in the Gulf of Palermo. The most polluted zones showed high metal concentrations, and low diversity of benthic foraminifera with species typical of stressed environments. By contrast, the lowest polluted zones showed a high population density and the highest percentages of epiphytes. Epiphytes were abundant where a Posidonia oceanica meadow was present and decreased in the most polluted zones. Sediments of the Gulf of Termini and Lampedusa exhibited high percentages of benthic foraminifera typical of well-oxygenated waters and low concentrations of metals, with the exception of sites located near sewage outfalls and harbour areas. Furthermore, even though deformed tests are commonly known in natural stressed environmental conditions, this study shows that in the most polluted zones, benthic foraminifera were characterised by the highest percentages of deformed individuals.