It is great to see many runners now running barefoot or in minimalist shoes. Running barefoot is great for strengthening the support structures of the foot and at the same time, developing better running technique. However, many runners are also experiencing negative consequences such as stress fractures from running barefoot or in minimalist shoes.
The main reason for this is that they do not adequately prepare themselves for the barefoot running. As should be well known, whenever you undertake a new activity or do something drastically different in the same activity, you should first prepare the body physically to withstand the forces that will be encountered that are new and different.
In other words, you should do exercises to strengthen the muscles that will be used in a new activity in the same manner as they are displayed during execution of the new activity. In this case it means strengthening the muscles of the foot arch and the other support structures of the foot.
This means doing exercises such as marble pickups, towel toe curls, ball of the foot walking and jogging, inversion and eversion and toe raises. Understand that when you run in shoes, most shoes have a built-in arch that prevents the foot from functioning normally. As a result most of the muscles of the foot become weakened after a period of time and are no longer capable of carrying out the functions that are normally associated with them.
It is also a fallacy to believe that running strengthens all the muscles in the body that are involved in running. This happens initially when you first out running but then it levels off and you only maintain the same level of strength to enable you to run at the same pace for the same distance for the same number of times per week or month. This is why injuries occur to many runners when they increase their mileage without first preparing themselves for the increases.
Thus barefoot running is great for most runners. However, for you to get the maximum benefit from barefoot running you should prepare yourself in advance where specific strength exercises for the foot and foot structures. This will help prevent injuries and most importantly, will enable you to run longer distances more efficiently and faster.
For more information on barefoot running, running technique and exercises specific to running see the Second Edition of Explosive Running.