BackgroundStudying natural, complex behaviours over a range of different species provides insights into the evolution of the brain and behaviour. Whisker movements reveal complex behaviours; however, there does not yet exist a protocol that is able to capture whisker movements and behaviours in a range of different species. New methodWe develop a new protocol and make recommendations for measuring comparative whisker movements and behaviours. Using two set-ups – an enclosure camera set-up and a high-speed video set-up - we capture and measure the whisker movements of sixteen different captive mammal species from four different animal collections. ResultsWe demonstrate the ability to describe whisker movements and behaviours across a wide range of mammalian species. We describe whisker movements in European hedgehog, Cape porcupine, domestic rabbit, domestic ferret, weasel, European otter and red fox for the first time. We observe whisker movements in all the species we tested, although movement, positions and behaviours vary in a species-specific way. Comparison with existing method(s)The high-speed video set-up is based on the protocols of previous studies. The addition of an enclosure video set-up is entirely new, and allows us to include more species, especially large and shy species that cannot be moved into a high-speed filming arena. ConclusionsWe make recommendations for comparative whisker behaviour studies, particularly incorporating individual and species-specific considerations. We believe that flexible, comparative behavioural protocols have wide-ranging applications, specifically to better understand links between the brain and complex behaviours.