Fermentation of milk is considered to improve ease of digestion. The protein composition of sheep milk differs from cow milk. We hypothesized that sheep milk would produce bioactive properties with different effects on gastrointestinal (GI) motility compared with cow milk and that this would also differ following fermentation. We compared the effect of sheep and cow milk drinks, pre and post fermentation, fed to rats over two weeks, on the rate of GI transit of beads over 12-hours using X-ray imaging. Stomach emptying in animals fed sheep yoghurt was more complete than that for cow yoghurt. GI transit was increased for sheep milk treated animals than for cow milk, and colonic transit was increased, with a similar pattern observed for the yoghurts. The increased colonic transit for sheep milk compared with cow milk reveals prominent species differences, regardless of whether or not the milk was fermented.