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The extent to which marine species avoid survey vessels is the subject of considerable debate, with stimuli such as noise and pressure waves receiving particular attention. By some estimates, avoidance behaviour is a major bias in the assessment of pelagic species distribution and density. Surveyors of the marine environment are increasingly using autonomous platforms; thus the question of avoidance of these novel platforms must be considered. A long-duration, underwater glider with an integrated echo-sounder was deployed to measure the density and distribution of Antarctic krill. We show that krill reacted to the glider, despite the low-noise profile of the platform. The weighted-mean depth of krill swarms was observed to deepen when a glider came within 30 m. In addition, we observed a near-range decrease in depth-integrated acoustic backscatter and we demonstrate that this effect is not explained by the instrument's acoustic footprint. The potential triggers for these behaviours are discussed. The list of sensors available for use on a glider is increasing, with some producing sound, light or other potential stimuli for behavioural response. Our paper demonstrates that caution should be used when designing mission payloads and in the interpretation of acoustic data for animal density from gliders. A key consideration for surveyors may be the factoring in of an exclusion zone from their analyses.