Hip alignment is a concern because it--or rather the functional leg-length discrepancy it tends to introduce--is a source of many potential injuries. If you can visualize the impact of running with one leg slightly longer than the other, you may be able to imagine some of the injuries listed below.
On the "longer leg" (raised side of the hip), which experiences greater impact and torsional forces, runners can experience:
• Hip injuries or soreness: This seems the most obvious, as the increased force of impact is transmitted all the way up to the hip.
• Hamstring strains and piriformis syndrome: The longer leg can end up bearing slightly more of the work in propelling you forward, thus making the hamstring more vulnerable to strains.
• IT Band Syndrome: ITBS is seen increasingly as an issue originating from weak hips and glutes, but the increased loads from a seemingly longer leg can have the same effect.
• Patellofemoral Pain Syndrome (Runner's Knee): The knee is another joint that bears excessive forces on the longer leg, and can therefore be subject to injury.
On the "shorter leg" (lowered side of the hip), which typically ends up experiencing more of a midfoot landing, the most common issue is Achilles tendinitis (or plantar fasciitis).