Advances in molecular genetics and in vivo ocular imaging modalities have enhanced our understanding of the corneal dystrophies. To date at least 11 genes have been identified, in which mutations manifest in corneal disease. In addition there are at least eight other loci identified to which corneal dystrophies have been linked. The information gained from the knowledge of gene function, aberrant protein production, or altered enzyme activity in the cornea, has resulted in greater knowledge of the pathophysiological mechanisms in these disorders. In vivo confocal microscopy has recently enabled microstructural study of dystrophic corneas throughout the disease course, rather than being limited to histopathological analysis of tissue removed at corneal transplantation. This perspective article summarizes the current knowledge, with emphasis on the genes, mutant proteins and resultant mechanisms that lead to manifestations of disease, along with characteristic findings with in vivo confocal microscopy.