I did a bit of research on barefoot running. The data is primarily from studies published in core medical journals. The results are presented below:

Humans have engaged in endurance running for millions of years, but the modern running shoe was not invented until the 1970s. For most of human evolutionary history, runners were either barefoot or wore minimal footwear such as sandals or moccasins with smaller heels and little cushioning relative to modern running shoes. This makes one wonder as to how runners coped with the impact caused by the foot colliding with the ground before the invention of the modern shoe. Prof. Daniel E. Lieberman and his team from the Harvard University have been investigating the biomechanics of endurance running, comparing habitually barefoot runners with runners who normally run in modern running shoes with built-up heels, stiff soles and arch support. Their research has shown that  habitually barefoot endurance runners often land on the fore-foot (fore-foot strike) before bringing down the heel, but they sometimes land with a flat foot (mid-foot strike) or, less often, on the heel (rear-foot strike). In contrast, habitually shod runners mostly rear-foot strike, facilitated by the elevated and cushioned heel of the modern running shoe. Kinematic and kinetic analyses show that even on hard surfaces, barefoot runners who fore-foot strike generate smaller collision forces than shod rear-foot strikers. This difference results primarily from a more plantarflexed foot at landing and more ankle compliance during impact, decreasing the effective mass of the body that collides with the ground. Forefoot and some mid-foot strikers hit the ground in a way that generates almost no collision forces even on hard surfaces like steel.

Evidence that barefoot and minimally shod runners avoid rear-foot strike with high-impact collisions may have public health implications. The average runner strikes the ground 600 times per kilometre, making runners prone to repetitive stress injuries. The incidence of such injuries has remained considerable for 30 years despite technological advancements that provide more cushioning and motion control in shoes designed for heel–toe running. Although cushioned, high-heeled running shoes are comfortable, they limit proprioception and make it easier for runners to land on their heels. Furthermore, many running shoes have arch supports and stiffened soles that may lead to weaker foot muscles, reducing arch strength. This weakness contributes to excessive pronation and places greater demands on the plantar fascia, which may cause plantar fasciitis.

There have been other interesting findings about barefoot running reported in peer reviewed medical journals.

A study by Hanson and colleagues (2011) investigated the oxygen cost of running barefoot vs. running shod on the treadmill as well as over ground. 10 healthy recreational runners, 5 male and 5 female, whose mean age was 23.8±3.39 participated in the study. Subjects  participated in 4 experimental conditions: 1) barefoot on treadmill, 2) shod on treadmill, 3) barefoot over ground, and 4) shod over ground. For each condition, subjects ran for 6 min at 70% VO₂ max pace while VO₂, heart rate and rating of perceived exertion were assessed. An assessment of results revealed that running with shoes showed significantly higher VO₂ values on both the treadmill and the over ground track. Heart rate and rating of perceived exertion were significantly higher in the shod condition as well. For the over ground and treadmill conditions, recorded VO₂ while running shod was 5.7% and 2.0% higher than running barefoot. It was concluded that at 70% of VO₂ max pace, barefoot running is more economical than running shod, both over ground and on a treadmill.

Dr Kerrigan and colleagues (2009) who compared the effects on hip, knee and ankle joints of running barefoot versus running in modern running shoes, concluded that running in shoes exerted more stress on these joints compared to running barefoot or even walking in high-heeled shoes. They observed that, compared with barefoot running, running with running shoes resulted in:

* Increased joint torques at the hip, knee and ankle.

* Disproportionately large increases in the hip internal rotation torque and in the knee flexion and knee varus torques.

* On average these torque increases were: 54% in hip internal rotational, 36% in knee flexion, and 38%  in knee varus.

The researchers concluded that while typical running shoes support and protect feet quite well, they increase stress on the hips, knees and ankles, and this is likely to be caused by an elevated heel and extra material under the medial arch.

A 2009 study by Squadrone & Gallozzi in experienced barefoot runners found that compared to the standard shod condition when running barefoot the athletes landed in more plantarflexion at the ankle. This caused reduced impact forces and changes in stride kinematics. In particular, significantly shorter stride length and contact times and higher stride frequency were observed. Compared to standard shod condition, VO₂ and peak impact forces were significantly lower. This study also found that lower limb kinematics with Vibram Fivefingers was similar to barefoot running with a foot position which was significantly more plantarflexed than in control shoe.

The mechanical modifications of running showed that the main role of the shoe was to attenuate the foot-ground impact by adding damping material. However, according to Divert  and colleagues (2008), these changes may lead to a decrease of the storage and restitution of elastic energy capacity which could explain the lower net efficiency reported in shod running.

The opponents of barefoot running, however,  feel that the benefits of barefoot running are being oversold. Running barefoot on extremely hot pavement or in extremely cold weather might damage the soles of the feet. Then there are nails and glass and pebbles and other objects that can puncture the soles of feet or lead to stubbed toes. And even if heel strikes are eliminated by running barefoot, shorter strides means the feet hit the ground more often, so what’s gained by reducing the force of impact might be offset by the increase in frequency of impact.

So is running barefoot a passing fad?. It does not appear so. With the ever increasing numbers of runners, barefoot running is here to stay.

Does barefoot running cause less injury? The jury is still out. Prof. Daniel E. Lieberman says "While there are anecdotal reports of barefoot runners being injured less, there is very little scientific evidence to support this hypothesis at this time. Well-controlled studies are needed to determine whether barefoot running results in fewer injuries."

"The key thing is not being barefoot, but using a barefoot style, and not colliding into the ground with your heels” he adds

References

Divert C, Mornieux G et al. Barefoot-shod running differences: shoe or mass effect? Int J Sports Med. 2008 Jun;29(6):512-8

Hanson NJ, Berg K et al. Oxygen cost of running barefoot vs. running Shod. Int J Sports Med. 2011 Jun;32(6):401-6. Epub 2011 Apr 6.

Kerrigan DC, Franz JR, Keenan GS et al. The effect of running shoes on lower extremity joint torques. PM R. 2009 Dec;1(12):1058-63.

Lieberman DE, Venkadesan M, Werbel WA etc. Foot strike patterns and collision forces in habitually barefoot versus shod runners. Nature. 2010 Jan 28;463(7280):531-5.

Squadrone R, Gallozzi C. Biomechanical and physiological comparison of barefoot and two shod conditions in experienced barefoot runners. J Sports Med Phys Fitness. 2009 Mar;49(1):6-13.