The cornea is the eye’s first optical surface, avascular and transparent, covered externally by a stratified epithelium that constantly renews itself. Disruption in this renewal compromises transparency, potentially leading to vision loss. The corneal surface is protected and nourished by the tear film, which contains growth factors vital for corneal maintenance and maturation. Tear composition and function are increasingly well understood. A deeper understanding of lacrimal pathophysiology is essential to developing regenerative therapies for tear gland deficiencies and ocular surface abnormalities. Proteomic analysis of tears enables comprehensive, unbiased evaluation in both normal and pathological states. The transcription factor PAX6 is essential for normal eye development, including the lacrimal gland. Mutations in PAX6 are associated with a range of ocular malformations such as aniridia, anterior segment dysgenesis, dominant keratitis, coloboma, optic nerve hypoplasia, persistent fetal vasculature, and microphthalmia. Some patients also show non-ocular symptoms. In patients with PAX6 mutations, the cornea often shows progressive limbal stem cell deficiency, evolving from peripheral keratopathy to total corneal opacification and fibrosis. Chronic inflammation and tear film abnormalities are frequent and contribute to disease progression. Current treatments for dry eye in these patients are non-specific and include artificial tears, cyclosporine eye drops, punctal plugs, or scleral lenses. Identifying specific qualitative abnormalities in the tear film represents a necessary first step toward developing targeted therapies, such as protein-based eye drops to preserve the cornea in patients with PAX6-related ocular malformations.