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Keratoconus is a corneal disease characterized by corneal ectasia, progressive corneal thinning, conical protrusion and irregular astigmatism. Several studies have indicated that keratoconus is a complex disease with genetic heterogeneity. Genetic studies on keratoconus involving nuclear genome, mitochondrial genome and epigenetics were increasing. This article reviews the recent progress in genetic research on keratoconus.