Lens coloboma is a developmental defect resulting from abnormalities of the zonules and ciliary body. It may present as an isolated pathology or be accompanied by anomalies in different ocular structures. We report the case of a 20-year-old man referred for evaluation of anisometropic amblyopia in the right eye. Manifest refraction was −2.25 +3.00 ×35 in the right eye; corrected distance visual acuity, 20/50. Corneal topography revealed regular astigmatism of +2.46 D at 124°, and wavefront aberrometry revealed an irregular internal astigmatism of +6.27 D at 35°. Only after full pupillary dilation was a peripheral lens coloboma observed. This case demonstrates that even minor distortions of clear and normally positioned lenses may lead to amblyopia and raises the possibility that corneal changes may occur developmentally through the process of emmetropization partly to compensate for lenticular astigmatism arising from the coloboma.