Meiofauna assemblages of three Italian Marine Protected Areas (MPAs), Miramare (Trieste, Friuli-Venezia Giulia), Porto Cesareo (Lecce, Apulia) and Capo Caccia (Sassari, Sardinia), were investigated. Sediment samples were collected during summer 2005 in the shallow subtidal (1-4 m depth). The meiofauna was primarily represented by Nematoda and Copepoda. The results showed that significant differences in meiofauna communities abundances were found among the three Italian MPAs, and in particular between Capo Caccia and Porto Cesareo (3840 ± 422 SE individuals·10 cm -2 at Miramare, 5716 ± 857 SE ind.·10 cm -2 in Porto Cesareo, and 1063 ± 289 SE ind.·10 cm -2 in Capo Caccia). These differences were mainly due to a clear change in nematodes and copepods abundances in the two MPAs. Meiofauna diversity was not significantly different among the three MPAs. The analysis on nematode communities showed a dominance of deposit feeders in Porto Cesareo (Anoplostoma, Daptonema and Theristus), while in the marine reserves of Miramare and Capo Caccia epigrowth feeding nematodes, and predators/omnivores were dominant (Mesacanthion, Marylynnia). The results reported here represent a new contribution to the knowledge of the Mediterranean meiofauna and nematode assemblages structure and composition.