Objectives: To report a novel SOX2 (OMIM 184429) mutation in a Chinese family and to describe its ocular and extraocular clinical features. Methods: Ocular and systemic examinations were performed, and genomic DNA was prepared from peripheral leukocytes. The coding exons and the adjacent intronic sequence of SOX2 were analyzed by cycle sequencing. Results: A novel heterozygous c.695CϾA (p.Thr232Asn) mutation in SOX2 was identified in a Chinese family in which both the father and the son had iris and chorioretinal uveal colobomas. In addition, cataracts were noted in the father but not in the son. Other anomalies were not found in the father but were present in the son, including brain arachnoid cyst, microcornea, retrobulbar colobomatous orbital cyst, and penoscrotal hypospadias. This mutation was not detected in the unaffected mother and 103 unaffected control individuals. Conclusions: Mutation in SOX2 is associated with typical ocular coloboma and probably other anomalies in this Chinese family. Arachnoid cyst has not been reported in individuals with the SOX2 mutation. Clinical Relevance: The results remind us that ocular coloboma may be accompanied by arachnoid cyst and may be associated with SOX2 mutation, which will be helpful for improving diagnosis and patient care.