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As Wyatt mentions, what you are experiencing is probably muscular strain. It’s quite natural, as you actively use your eyes to adjust the mouse pointer position, which means you use the eye muscles in ways you are not used to yet.
As pointed out in the FAQ article, the light used in the eye tracker meets european standards for optical radiation hazards (IEC/EN 62471), and has been tested not to be harmful.
I have spent 4 years working with our Assistive Technology products. Over the years, Tobii has sold thousands of eye-trackers to users with various disabilities. These devices are mainly used as an alternative communication method, meaning that users are dependant on their devices throughout their entire day. Typically, these users have severe physical disabilities that prevent them from interacting with the computer through other interaction methods than gaze. In other words we have thousands of people that use our eyetrackers as their primary tool for face-to-face communication, surfing the web, writing documents, controlling their home, writing text messages/emails and everything else you would want to do on a computer. The devices are usually mounted on the persons wheelchair and goes wherever the user goes, so they actively use their devices or have the device in front of them for the vast majority of their day.
On a daily basis, these people use our eye trackers far more than any developer would, and we have not had any reports that the light on our eye trackers have affected or done damage to any of our users.