I'm in the process of trying to transition into my Vibrams and it's very hard. Most noticeable things are the calf soreness and blisters under the ball of my feet from lack of padding. Some people have ankle pain because they lack strength there too.
Make sure that if you do decide to take the plunge, you start out slowly. As in, give it about at least 2 months to be able to run 3 miles in them, unless you have previous exposure to running barefoot or minimalist. It is very tempting to run longer in them, because you honestly feel lightweight and faster, but don't do it :P I did a 4 mile run my first time out and could not walk for a week.
I will say that it corrected my running in that I can midsole and front-feet strike even in my structured sneakers now.



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