The identification of the genetic basis of approximately half of the corneal dystrophies in the past decade has resulted in significant advances in our understanding of the genetic control of corneal clarity and has provided clinicians with a definitive means to confirm or refute presumptive clinical diagnoses. This article serves as a guide to understanding the genetic basis of the corneal dystrophies and provides a revised anatomically based classification system that is intended for the clinician, who must possess a working knowledge of the molecular genetic basis of the corneal dystrophies to accurately diagnose, counsel, and manage the disease in affected patients.