Abstract Autonomous reflexes enable animals to respond quickly to potential threats, prevent injury andmediate fight or flight responses. Intense acoustic stimuli with sudden onsets elicit a startle reflex while stimuli ofsimilar intensity but with longer rise times only cause a cardiac defence response. In laboratory settings,habituation appears to affect all of these reflexes so that the response amplitude generally decreases with repeatedexposure to the stimulus. The startle reflex has become a model system for the study of the neural basis of simplelearning processes and emotional processing and is often used as a diagnostic tool in medical applications.However, previous studies did not allow animals to avoid the stimulus and the evolutionary function and long-term behavioural consequences of repeated startling remain speculative. In this study we investigate the follow-upbehaviour associated with the startle reflex in wild-captured animals using an experimental setup that allowsindividuals to exhibit avoidance behaviour.Results:We present evidence that repeated elicitation of the acoustic startle reflex leads to rapid and pronouncedsensitisation of sustained spatial avoidance behaviour in grey seals (Halichoerus grypus). Animals developed rapidflight responses, left the exposure pool and showed clear signs of fear conditioning. Once sensitised, seals evenavoided a known food source that was close to the sound source. In contrast, animals exposed to non-startling(long rise time) stimuli of the same maximum sound pressure habituated and flight responses waned or wereabsent from the beginning. The startle threshold of grey seals expressed in units of sensation levels wascomparable to thresholds reported for other mammals (93 dB).Conclusions:Our results demonstrate that the acoustic startle reflex plays a crucial role in mediating flightresponses and strongly influences the motivational state of an animal beyond a short-term muscular response bymediating long-term avoidance. The reflex is therefore not only a measure of emotional state but also influencesemotional processing. The biological function of the startle reflex is most likely associated with mediating rapidflight responses. The data indicate that repeated startling by anthropogenic noise sources might have severeeffects on long-term behaviour. Future, studies are needed to investigate whether such effects can be associatedwith reduced individual fitness or even longevity of individuals.