The effect of boat noise on the behaviour of bluefin tuna Thunnus thynnus was investigated in the Egadi Islands, Sicily, during spring 2005 using a fixed tuna trap set near shipping routes. Tuna behaviour was observed when exposed to both natural ambient sound and sound generated by hydrofoil passenger ferries, small boats and large car ferries. Acoustical and behavioural analyses were conducted with and without extraneous sound to define a list of behavioural categories. Each vessel produced different engine sounds with regard to their composition and bandwidth, and all were distinctly different from ambient sound levels. In the absence of boat noise, tuna assumed a concentrated coordinated school structure with unidirectional swimming and without a precise shape. When a car ferry approached, tuna changed swimming direction and increased their vertical movement toward surface or bottom; the school exhibited an unconcentrated structure and uncoordinated swimming behaviour. Hydrofoils appeared to elicit a similar response, but for shorter periods. Agonistic behaviour was more evident when exposed to sounds from outboard motors of small boats. This study showed that local noise pollution generated by boats produced behavioural deviations in tuna schools. Schooling enhances tuna homing accuracy during their spawning migration, and an alteration in schooling behaviour can affect the accuracy of their migration to spawning and feeding grounds.