To compare the anterior segment indices between mentally retarded and normal children. The current study was conducted as a cohort. In this study, 73 mentally retarded and 76 normal children were selected from normal school and special schools for mentally retarded children using random cluster sampling method. Mental retardation in children was confirmed by a psychologist. Optometry examinations including visual acuity and refraction were performed for all participants, and ultimately, corneal imaging measurements were taken by Pentacam. The mean age of mentally retarded and normal children was of 13.30 ± 1.83 and 13.05 ± 1.82 years, respectively (P = 0.180). A multiple generalized estimating equations model demonstrated that there is a significant association between central corneal thickness (CCT) (coef = 1.011, P < 0.001), corneal diameter (CD) (coef = 0.444, P = 0.046), anterior chamber depth (ACD) (coef = 0.23), P < 0.001) and index of vertical asymmetry (IVA) (coef = 0.12, P < 0.001) and mental retardation. Cerebral palsy children had higher keratoconus index (KI), central keratoconus index (CKI), index of height asymmetry(IHA), and index of height decentration (IHD) compared to those without cerebral palsy (P < 0.05). Children with moderate mental retardation had higher index of surface variance (ISV), IVA, IHA, and IHD than those with mild mental retardation (P < 0.05). The mean and standard deviation of CCT, CD, ACD and IVA index in mentally retarded children were 535.3 ± 46.68 micron, 11.87 ± 0.42 mm, 3.29 ± 0.24 mm and 0.25 ± 0.18 mm, respectively. These indices in the normal group were 525.53 ± 47.52 micron, 11.84 ± 0.38 mm, 3.15 ± 0.28 mm and 0.17 ± 0.05 mm, respectively. The findings of this study showed that some anterior segment indices were different in mentally retarded compared to normal children. Moreover, some keratoconus indicators were worse in cerebral palsy children and children with higher grade mental retardation. So, it is important to consider keratoconus screening in these children.