AIM: To evaluate association between mutations in the visual system homeobox 1 (VSX1) gene and keratoconus (KCN) complicated with granular corneal dystrophy (GCD), direct sequencing was performed in an Iranian family affected by KCN and GCD in four generations.METHODS: An Iranian pedigree with keratoconus spanning four generations along with GCD was identified.Whole blood sample was used for genomic DNA extraction.The molecular analysis by using polymerase chain reaction (PCR) of the entire coding region and intron-exon boundaries of VSX1 gene was preformed to investigate the possible linkage between KCN and GCD.Subsequently, direct sequencing was used for PCR products and mutation analysis was conducted in the patients and controls.RESULTS: Mutation analysis in VSX1 gene did not detect evidence for association between KCN and GCD diseases and VSX1 gene.Our data excluded VSX1 as the disease-causing gene for KCN/GCD in this specific pedigree.CONCLUSION: Despite of no association between KCN patients with GCD and VSX1 gene variations, other probable genes involved in pathogenesis of the KCN and GCD diseases need to be investigated in the patients.