If you aren't aware of your form and your stride, any kind of running, shoe or no, will cause injuries. When you begin to slouch or lean when tired, you will get back and hip injuries. If your stride is off balance due to a dominant leg, you will see quad and hamstring issues. If your allow your feet to turn outward, indicating weaker quad muscles, you will see knee and IT issues.
It has been my experience running barefoot and with 5 finger shoes that I am more aware of my form, how my feet strike and where, and when during my runs my form is most vulnerable. This has allowed me to make my running (yes in shoes) more effective and less painful/sore. Because of all of the bullheads (nasty little stickers that even the Vibrams can't overcome) and potential for rattlers, I run mostly in shoes. But if I run on the treadmill, I'll go barefoot or in socks. I like to hike barefoot, too, and have found some great trails full of sand, rocks, and mud that are awesome! And with only a few pine needles to overcome, which, thanks to the bullheads, aren't big thorns in my paws!
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