Here is an extract from a study published on the web site sportscience regarding barefoot running.
Running barefoot is associated with a substantially lower prevalence of acute injuries of the ankle and chronic injuries of the lower leg in developing countries, but well-designed studies of the effects of barefoot and shod running on injury are lacking. Laboratory studies show that the energy cost of running is reduced by about 4% when the feet are not shod. In spite of these apparent benefits, barefoot running is rare in competition, and there are no published controlled trials of the effects of running barefoot on simulated or real competitive performance.