During the first part of the cover test, the unilateral cover test, you will be asked to focus on a distant object, such as a single letter on an eye chart. (You will be instructed to keep your glasses on, if you have them.) The practitioner will cover your right eye with an occluder while watching for movement from the left, then do the same by covering your left eye. If your uncovered eye moves in order to fixate on the letter or object, then you may have strabismus or an eye turn.
The second part of the cover test is the alternating cover test. The occluder will be switched from one of your eyes to the other. The practitioner will be watching to see if your eye moves after it is uncovered, known as a phoria. Although some amount of phoria is normal, large amounts can cause eye strain, blurry vision or double vision, as you must make an effort to fixate both eyes on a target.
Your eye care practitioner can measure the amount of strabismus or phoria you have by holding prisms in front of your eyes while performing the cover test. These measurements will help determine how much power or prism is needed to help you see your best.
Elliott, David B. Clinical Procedures in Primary Eye Care, Pp 115-116. Elsevier Limited, 2003.