To investigate and compare the clinical outcome of primary penetrating keratoplasty in pediatric patients with Peters anomaly and sclerocornea. Medical records of 20 eyes of 18 patients with Peters anomaly or sclerocornea who underwent primary penetrating keratoplasty when they were 5 years or younger were reviewed. The survival rates and median survival times of corneal grafts were evaluated to determine the surgical outcome. Demographics of patients, the preoperative characteristics of recipient eyes, surgical procedures, causes of graft failure, and postoperative complications were analyzed to identify the factors affecting graft survival. A total of 20 penetrating keratoplasties were performed in 18 patients. Eight patients had Peters anomaly, and 10 patients had sclerocornea. Overall, 50% of corneal grafts survived during the follow-up of 92.7 ± 10 months. The graft survival was 65% at 6 months and remained 50% at 12 months, 2 years, and 5 years after surgery. The mean survival time and survival rate were significantly different between patients with Peters anomaly and those with sclerocornea (the survival time, 135.6 ± 17.9 vs. 36.4 ± 16.1 months, P = 0.014; the survival rate, 87.5% vs. 25.0%, P = 0.02). The presence of opacity or vascularization in the limbus and in the peripheral cornea and the diameter of the recipient cornea were significantly correlated with graft failure. Penetrating keratoplasty in patients who were 5 years or younger had an excellent surgical outcome in patients with Peters anomaly, whereas the graft survival was poor in patients with sclerocornea.