I hurt my rotator cuff from a bad fall while training a couple years back, then aggravated it with more weightlifting. I was really frustrated for awhile because it seemed to take so long to heal. The key to helping it recover was physical therapy, but first you'll need an x-ray to make sure there is no bone damage. If you go to see your primary-care physician they can get you an x-ray right off the bat and give you information about physical therapy that you can do on your own. If your doctor is any good they also might be able to give you an idea of what kind of shoulder injury it could be, by lifting your arm up and applying force in different directions. The PT is key for regaining strength and helping it to heal quicker and it is possible you may be able to incorporate it into your normal workout routine and not have to stop training so much. Here are some basic rotator cuff exercises:
http://familydoctor.org/265.xml
I still do these and others to this day to keep the rotator cuff strengthened. If PT doesn't help eventually your doctor may recommend an MRI to look at some softer tissue damage, but they are very expensive and your doctor may opt to exhaust all other possibilities first.