Barn owl pellets were analyzed for comparing the small mammal fauna among three islands of Tuscan archipelago, Italy. Rarefaction analyses and diversity analyses were used on barn owl pellet samples at a total of 18 sites. Apodemus sylvaticus appeared the most abundant species in Elba and Capraia, and Mus musculus in Pianosa. Diversity profiles showed that Pianosa and Elba were very similar in terms of dominance and evenness profiles, whereas Capraia had higher dominance and lower evenness. Using our original data and literature review, we found that 5 species are found in Pianosa, 1 in Giannutri, 0 in Montecristo, 5 in Giglio, 7 in Elba, 6 in Capraia, and 1 in Gorgona. There was no effect of island area, human population size, or linear distance from mainland on species richness.