Sediment samples were collected from four sandy and muddy bottom sites at both Sacca di Goro lagoon (northern Adriatic Sea) and Lesina lagoon (southern Adriatic Sea) on one occasion in May and one occasion in July in order to make a comparative study of ciliate abundance and diversity. The temperature, pH, dissolved oxygen, and redox potential were measured at the time of collection, the water content of the sediments was determined, and samples subjected to granulometric analysis. The ciliated protozoa in sub-samples from the top centimeter of sediment were identified to genus and species level and enumerated. Ciliates belonging to 38 and 33 species were found in the sediment of Sacca di Goro and Lesina, respectively, the diversity of ciliates varying widely between stations. Total ciliate numbers ranged from 32 to 759 cm(-2) and from 2 to 256 cm(-2) at Sacca di Goro and Lesina, respectively; the ciliate biomass ranged from 1.1 to 30.3 microg C cm(-2) in the samples collected at Sacca di Goro, and from 0.01 to 157 microg C cm(-2) in the samples collected at Lesina lagoon. Aspidisca lynceus, Aspidisca steini, Chilodonella uncinata, Frontonia marina, Pleuronema marinum, Strombidinopsis minimum, Strombidium sp., and Urotricha sp., were observed at the two lagoons but not in all stations; Keronopsis flavicans and Trachelostyla pediculariformis were often numerous at Goro lagoon, A. lynceus, Condylostoma patulum and Tracheloraphis teissieri were the most abundant ciliates observed at Lesina lagoon.