The ocular surface is often affected by organ-specific or systemic diseases of a congenital or metabolic nature. This chapter gives a review on metabolic and congenital disorders showing ocular surface manifestations of each disorder. It also provides a synopsis of selected diseases with the extensive tables that will summarize the different disorders as well as inheritance pattern, gene/locus, enzyme product, corneal manifestations and treatment. The metabolic and congenital disorders that affect ocular surface discussed are cystinosis, tyrosinemias, alkaptonuria, amyloidosis, GOUT (hyperuricemia), xeroderma pigmentosum, systemic mucopolysaccharidoses and mucolipidosis.