AIM: To evaluate the graft rejection and visual outcomes after penetrating keratoplasty (PK) in the presence of various congenital corneal opacities in children. METHODS: In this retrospective cohort study, children who underwent PK were then followed for 5y. The patient’s medical records were collected from June 2014 until June 2019 and analyzed in December 2019. All patients were children under three years old with congenital corneal opacities with or without microcornea who came to a pediatric ophthalmologist and underwent PK in Jakarta Eye Center (JEC). Beforehand, all children have participated in a thorough evaluation for PK. In the case of severe microcornea was not advised to undergo surgery. The visual outcomes and graft survival rate were described in percentages. The graft survival plot was presented with Kaplan-Meier, while the visual acuity was analyzed using the Wilcoxon signed ranks test. RESULTS: Sixteen eyes from eleven patients (seven girls and four boys) underwent PK. The graft survival rate of the first 6, 12, and 18 mo later of keratoplasty was 100%, 83.3%, and 66.7%, respectively. The overall mean survival time is 22mo (standard error 2.419), and no significant difference between the patients underwent PK before and after 36mo of their age (P=0.52). The graft failure was 50%, and post-surgery complications included cataract 43.7%, band keratopathy 12.5%, and scleromalasia 6.25%. Wilcoxon test analysis of visual acuity post keratoplasty was not statistically significant (P=0.34), while overall showed 44% improvements of visual outcome for 5y of follow-up. With a good survival at one year up to 22mo (83.3%), the visual acuity could be achieved (63%), and showed improvements (44%) during follow-up. CONCLUSION: The complications are frequent for pediatric PK. Thus, corneal surgery on infants requires careful case selection, adequate pre-operative evaluation, skilled surgery (optical correction), very close cooperation family–physician, intensive post-operation care, and amblyopia management in the future.