Corneal disorders are important factors causing visual loss, a major disability in humans. Several corneal disorders can be inherited and some are found to be resulted from genetic defects. Congenital hereditary endothelial dystrophy (CHED2) is an inherited corneal disorder with the disease onset at birth or early childhood. Recently mutations in the sodium bicarbonate transporter-like solute carrier family 4 member 11 (SLC4A11) have been identified in individuals with CHED2. Corneal abnormalities can also be found in some inherited storage diseases. Mucopolysacchridosis type I (MPS I) is an autosomal recessive lysosomal storage disorder caused by a deficiency of the enzyme alpha-L-iduronidase (IDUA). As a result of defects inside the lysosomes, accumulation of partially degraded glycosaminoglycans, heparan and dermatan sulfate leads to the progressive cellular dysfunction. MPS I has been classified into three clinical phenotypes with different severity and age of onset. Hurler syndrome (MPS IH) is the most severe with symptoms including severe developmental delay, hepatosplenomegaly, skeletal deformities and corneal clouding. The IDUA gene is found to be responsible for MPS I. Cystinosis is another autosomal recessive disorder characterized by defective transport of cystine across the lysosomal membrane and resulting in ophthalmic, renal, and other organ abnormalities. Here, we identified two novel pathogenic mutations in a Thai family with CHED2. The newly identified c.778A>G (p.K260E) mutation was inherited from the mother and was not identified in 100 ethnic-matched unaffected control chromosomes. The lysine residue at codon 260 was highly conserved. The 68-kb deletion encompassing the whole SLC4A11 gene was inherited from the father. This is the first study to describe the largest deletion in patients with CHED2. Further analysis to identify such deletion in the previously reported CHED2 patients with undetected SLC4A11 mutations using conventional PCR-sequencing technique is warranted. We also reported two Thai patients: one with Hurler syndrome, the most severe form, and the other with Scheie syndrome (MPS IS), the mildest. Mutation analyses revealed that the MPS IH patient was homozygous for a previously reported mutation, c.252insC, while the MPS IS patient was found to harbor a novel c.826G>A (p.E276K) mutation. When combined with the previous study in Thai MPS IH patients, the c.252insC mutant allele was found in 3 out of 6 alleles, accounting for 50 % of the mutations making it a possible common mutant allele for MPS IH in the Thai population. Transient transfection of the p.E276K construct into COS-7 cells revealed a significant reduction of IDUA activity compared to that of the wild-type IDUA suggesting it as a disease-causing mutation. Mutation analysis in the CTNS gene causing cystinosis was also performed. PCR sequencing of the entire coding regions of CTNS in six cystinosis patients from four families identified all eight mutant alleles, including two novel mutations, p.G309D and p.Q284X. This study expands the mutational and population spectrum of cystinosis. This study expands the mutational spectrum and emphasizes an important role of genetic testing for definite diagnosis, early initiation of appropriate therapy as well as genetic counseling in inherited corneal disorders.