A new classification of microphthalmos and coloboma is proposed to bring order to the complexity of clinical and aetiological heterogeneity of these conditions. A phenotypic classification is presented which may help the clinician to give a systematic description of the anomalies. The phenotype does not predict the aetiology but a systematic description of ocular and systemic anomalies improves syndrome identification. There are two major classes, total and partial microphthalmos, and a subclassification which follows the embryology of the anomalies. The aetiological classification consists of three classes: (1) genetic (monogenic and chromosomal), (2) prenatally acquired (teratological agents and intrauterine deformations), and (3) associations. Genetic disorders give rise to malformations; prenatally acquired anomalies are disruptions or deformations. The aetiological classification can be applied to other congenital birth defects and improves counselling of families. Recurrence risks vary considerably between the classes.