Glaucoma is a clinical entity with multifactorial etiology, a severe subtype occurs in infancy called primary congenital glaucoma (PCG). Three distinct levels interact sequentially to produce PCG: (i) genetic mutations mainly affecting the CYP1B1 gene, (ii) absence or dysregulation of a morphogen, and (iii) trabecular meshwork pathological changes either in patterning or remodeling. We will discuss these three levels in detail towards further understanding of the morphological basis of the disease, focusing on the missing points, for instance the exact nature and function of the morphogen along with the putative role of CYP1B1 gene.