A system and method are provided for measuring the thickness of a tear film layer and the heights of tear menisci around upper and lower eyelids of an eye. A plurality of images are acquired between consecutive blinks the eye using optical coherence tomography (OCT). The images depict the tear film layer and tear menisci as distinct from the cornea of the eye. In an embodiment, a plurality of reflectivity profiles from an OCT image are aligned and averaged. The difference between a first peak and a second peak of the average reflectivity profile is measured to determine the thickness of the tear film layer. The heights of the upper meniscus and the lower meniscus can also be measured from the same OCT image. In an embodiment, thickness measurements from the plurality of OCT images are combined. The measurements can be used to diagnose tear disorders, analyze treatments of dry eye and evaluate artificial tears.