Traumatic brain injury is considered one of the signature wounds of soldiers fighting in Iraq and Afghanistan, but the military medical system is failing to diagnose the injuries in many troops.

Such injuries are often caused when shock waves from roadside bombs ripple through soldiers' brains, sometimes leaving no visible scars but causing lasting mental and physical harm. Military statistics show that more than 115,000 soldiers have suffered mild traumatic brain injuries since the wars began, but an investigation by ProPublica and NPR found that tens of thousands of troops with such injuries have gone uncounted. And at Fort Bliss, one of the largest U.S. Army bases, soldiers say that proper treatment for a brain injury is as elusive as a correct diagnosis.

The Army's vice chief of staff, Gen. Peter Chiarelli, has defended the military's handling of those with brain injuries while acknowledging that the Army continues to have problems properly diagnosing such wounds. Meanwhile, congressmen from districts close to Fort Bliss have sent a letter demanding answers from base medical officials about the care being given to soldiers. And the leader of the Pentagon's premier program for treatment and research into brain injury unexpectedly stepped down from her post.

As we continued our investigation, we uncovered more troubling questions about the Pentagon's treatment of brain injury. We found that some commanders and doctors have denied brain-injured soldiers the Purple Heart, a sacrosanct military honor recognizing injury in combat. Though Army regulations specifically say that a mild traumatic brain injury, also known as a concussion, is eligible for the award, we found evidence that some military officials felt that such wounds were not serious enough to merit recognition.

We also discovered that the Pentagon's primary health plan, called Tricare, refuses to cover cognitive rehabilitation therapy, endorsed by many of the nation's top neurologists and medical groups as the best treatment for brain injury. Tricare commissioned a study which questioned the evidence for the treatment. But we uncovered secret internal criticism by top researchers who called Tricare's study "deeply flawed."

As our stories continued, so did the military's efforts to improve treatment. Soon after our initial pieces, the Pentagon announced a new policy that soldiers must have 24 hours rest after a concussion, and a complete neurological exam after suffering three concussions in a year. More than 70 U.S. senators and representatives demanded that Tricare provide cognitive rehabilitation to troops. Sen. Claire McCaskill, D-Mo., launched an investigation.

Most recently, Chiarelli announced that the Army is planning to issue new guidance on the award of the Purple Heart. Chiarelli acknowledged that our reporting had revealed the need for the new guidelines to make sure that no soldier is unfairly denied the medal. More soldiers may wind up with recognition. And the new guidelines, Chiarelli told us, will help the military establishment understand how serious brain injury can be.