The aim of this study was to determine the association between family history and corneal characteristics of keratoconus in Japan. The clinical records of patients with keratoconus who were interviewed regarding family history of keratoconus were retrospectively reviewed. Corneal indices derived from anterior segment optical coherence tomography were compared between the positive and negative family history groups using multiple linear regression analysis adjusted with age, sex, and history of atopy and eye rubbing. A total of 2,701 eyes, including 122 eyes with positive family history, were enrolled. Based on the adjusted multiple linear regression analysis, no significant differences were found between groups with and without a family history except for paracentral and mid-peripheral corneal thickness. The adjusted mean differences in paracentral and mid-peripheral corneal thicknesses between the two groups were -10.33 (95% confidence interval -20.29 to -0.37 P -value <0.05) and -9.78 (95% confidence interval -16.70 to -2.85, P -value <0.01), respectively. There was no significant association between family history and corneal indices in Japanese patients with keratoconus, except for paracentral and mid-peripheral corneal thicknesses. A Japanese patient with keratoconus who had a family history showed significantly lower paracentral and mid-peripheral corneal thicknesses than those with no family history.