Purpose: To describe clinical features of inferior rectus muscle aplasia in Japanese patients and to gain insight into its pathogenesis. Methods: Case presentation and literature review of 16 Japanese patients with inferior rectus muscle aplasia. Results: The age at presentation of 16 patients (9 females, 4 males, and 3 with unknown gender) varied from 7 months to 73 years (mean, 21.8 years). The inferior rectus muscle was absent on the right side in 10 patients, on the left side in 4 patients, and on both sides in 2 patients. Structural anomalies of the eye globe, such as microphthalmos, microcornea, and coloboma of varying degrees, were present on the ipsilateral side of the inferior rectus muscle aplasia in 4 patients and on the contralateral side in 1 patient. As surgical findings, anomalous inferiorly located insertion of the medial rectus muscle was discovered in 5 patients: 1 patient in association with microcornea and iris coloboma. Frequent surgical procedures were recession or tenotomy of the superior rectus muscle, combined with downward transposition of the entire or partial tendons of the medial rectus and lateral rectus muscle to the medial and lateral end, respectively, of the putative inferior rectus muscle insertion. Conclusions: The association of coloboma with inferior rectus muscle aplasia suggests that abnormal optic fissure closure during embryogenesis might underlie the muscle aplasia.