I have a mid-2011 MB Air, and whenever I use it for too long, I get some of the absolute worst migraines. I used to have a late 2008 MB (aluminum, not Pro) and I never had this problem. If I did, it wasn't that often. I can use other computers just fine, but my laptop is just torture sometimes. (My iPad and phone are fine, too.) Does anyone else get this? Is there something special about the screen that doesn't apply to others? I've turned brightness down, so it's not that.
If it's not the brightness, then most probably your shoulders and neck are being strained and are cramping/pressing on some nerves.
1st remedy: Take regular breaks and work out for a few minutes.
2nd remedy: have a professional take a look at your working position and environment (desk, chair, relative positioning of human and computer). Also you can set up a camera (still or video) to take pictures of you working (preferably from the side) and try to (for yourself) analyze your position.
3rd thing: If you're sharing your workspace with others, you may try to (carefully) ask whether others have been suffering as well * .
RGDS,
* This third thing is based on my friend's experiences. Around 2011 their whole company switched from windows PC's to macs. Around the same time a lot of people started complaining about illnesses, migraines, headaches, shortness of breath etc. Soon everyone started blaming the new computers - someone even cited the old apple-benzene -story. It was mayhem. A specialist was called in and after chasing down some futile avenues, the office was diagnosed as mold-infested
The company moved, the macs stayed. Now everyone's happy.