Keratoconus (KC) and chronic diabetes mellitus (DM) are both associated with significant defects in the human corneal structure. Studies have long suggested that DM is linked to KC, mainly via the crosslinking mechanism, but scientific evidences are lacking. The role of altered systemic metabolism is well-established in both DM and KC with studies suggesting localized altered cellular metabolism leading to the development of corneal pathologies. We have previously characterized the metabolic defects associated with both conditions using targeted metabolomics. To compare metabolic differences between KC and DM-derived corneal fibroblasts, we performed a respective study of two cohorts of the KC and DM populations using a retrospective analysis of targeted metabolomics data. The goal of this study was to identify the group of differentially regulated metabolites, in KC versus DM, so that we may unravel the link between the two devastating corneal pathologies.