Animation Rotating Problems

I'm using the following code to have my character run. But every time I let go of the WASD keys the player rotates 90 degrees clockwise.

function Update () 
{
    if(Input.GetAxis("Vertical") || Input.GetAxis("Horizontal"))
        animation.CrossFade("pistol_run");
    else
    {   
        animation.CrossFade("pistol_idle");
    }
}

Is it that my original animation file has the rotation wrong? If that is the case can I correct the animation within unity?