Southern resident killer whales numbered only 84 ind. in 2004. Disturbance by vessels may be a factor in the population's endangered status. To determine the importance of this factor, we compared behaviour in the presence and absence of vessels from 2003 to 2005 at 2 different sites along San Juan Island, Washington State, USA. Theodolite tracks were summarised in terms of swimming path directness and deviation indices, travel speed, and rates of respiration and surface active display behaviours. Vessel number and proximity were used in a generalised additive modelling framework as candidate explanatory variables for differences in whale behaviour, along with natural factors. Path directness varied with number of vessels and proximity to vessels. The increased distance that whales travelled in the presence of vessels could have resulted in increased energy expenditure relative to whales that could rest while waiting for affected whales to catch up. The likelihood and rate of surface active behaviour varied with number of vessels. Number and proximity of vessels were also related to variability in respiratory intervals, path deviation index and swimming speed. The high proportion of time that southern resident killer whales spend during summer in proximity to vessels raises the possibility that the short-term behavioural changes reported here may have biologically significant consequences.