We analyzed Spanish Collaborative Study of Congenital Malformations (ECEMC) data on a series of 1,124,654 consecutive births to study congenital eye malformations from an epidemiological standpoint. We studied their frequencies as well as some causal and clinical aspects. Four hundred fourteen infants had eye malformations, for an overall prevalence of 3.68/10,000 newborns. Most frequent were: anophthalmia/microphthalmia (21.34/100,000), congenital cataract (6.31), coloboma (4.89), corneal opacity (3.11), and congenital glaucoma (2.85). In our data, the tendency of eye malformations to be associated with other congenital abnormalities is evident (only 21.01% of cases were isolated). Eye defects are heterogeneous, since we have observed them in clinical patterns with all modes of inheritance or caused by different environmental agents. Chromosomal syndromes represent 60% of total syndromes, followed by syndromes of autosomal-recessive inheritance (15%), environmental syndromes (10%), autosomal-dominant syndromes (5.83%), and other types which have a lower frequency. Regarding defects associated with eye malformations, most frequent are limb anomalies (affecting 59.3% of multiply malformed cases), auricular/facial (47.1%), central nervous system (42.5%), osteomuscular excluding limbs (42.2%), genital defects (30.6%), oral clefts (29.4%), and the rest of the body systems, which are less frequent. Using the method outlined by Prieto and Martínez-Frías [1996: Am J Med Genet 62:61-67], it was demonstrated that the association of coloboma and anophthalmia/microphthalmia was specific, as was the combination of cataract and anophthalmia/microphthalmia, and that of anophthalmia/microphthalmia with holoprosencephaly. From these statistical associations some pathogenetic relationships in human embryos can be inferred, supporting several previously proposed mechanisms.