Running on a treadmill is quite different than running outside in that running on a treadmill does not require forward movement. Because running only affects vertical displacement, treadmill runners tend to wear more heavily on the heels of their shoes. Many of the top running shoe companies are making shoes designed specifically for running on a treadmill. These include more cushioning in the heel.
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One of the companies making a shoe specific to the treadmill is Asics, with its GEL-Treadmill. This shoe has more cushioning in the heel, particularly toward the outside, as treadmill runners tend to place more pressure on the lateral heel. Additionally, treadmill runners tend not to place as much pressure on the toes. Therefore, Asics limited the amount of gel in the toes to help make the shoes lighter. Finally, according to Asics website, vents in the sole increase circulation, and an "Impact Guiding System" encourages a natural gait.
LoveToKnow.com recommends a trio from Reebok. The Trinity KFS (Kinetic Fit System) has plenty of traction and provides support and flexibility. The Cushioning IV has lots of cushioning, hence its name, and has lots of mesh to help keep the foot cool. The Ultra KFS, much like the Cushioning IV, has ample cushioning in the sock liner and heel, which Reebok says will "soften the impact, allowing the runner to go for miles and miles."
LoveToKnow.com also recommends a couple of Nikes to help improve running on a treadmill. The Nike Zoom Equalon has an encapsulated heel and a "Zoom Air" unit, both of which provide lots of cushioning. Nike says the Zoom Equalon is a great shoe for those who over-pronate (roll their feet inward). The Air Max Moto was designed for distance runners who slightly under-pronate or slightly over-pronate; it is also built a little wider in the forefoot to provide comfort during a run.