As our understanding of phenotype has improved with improving anterior segment imaging, it has become increasingly clear that the early genotype-phenotype correlations were largely misled by inaccurate phenotyping. Using a novel classification, congenital or neonatal corneal opacification can be considered to be primary or secondary. Secondary corneal disease may be developmental or acquired. Genetic analysis using this phenotypic classification becomes easier to navigate. Primary corneal disease includes endothelial dystrophies, corneal dermoids, cornea plana, and CYP1B1 cytopathy. Genotyping for all these conditions is reasonably advanced. Secondary developmental corneal disease includes entities that are the least well understood genotypically. These are kerato-irido-lenticular dysgenesis (also known as Peters anomaly, types 1 and 2). The genotyping literature of these conditions is littered with confusion. Iridocorneal adhesions (Peters anomaly 1) are often avascular, whereas keratolenticular adhesions (Peters anomaly 2) are usually vascularized. Children with a known molecular diagnosis can have iridocorneal adhesion in one eye and keratolenticular adhesion in the other eye. This further supports the notion that Peters anomaly 1 or 2 is a sign and not a diagnosis. Further types of kerato-irido-lenticular dysgenesis are those in which the lens fails to form or forms and then degenerates. Genotyping in these cases has been somewhat more fruitful but, as always, not comprehensive. If the lens fails to form or forms partially, the gene involved is FOXE3, which is a lens gene. Not surprisingly, if the lens forms partially or fails to form, this has an effect on the vitreous and the drainage angle. These cases are often associated with severe glaucoma. Other secondary developmental corneal diseases may include Axenfeld-Rieger syndrome, Aniridia, and primary congenital glaucoma, all of which have specific genotypic characterization. Other secondary causes are acquired and include infection, trauma, and metabolic disorders.