This work evaluates changes in new morphogeometric indices developed considering the position of anterior and posterior corneal apex and minimum corneal thickness (MCT) point in keratoconus. This prospective comparative study included 440 eyes of 440 patients (age, 7-99 years): control (124 eyes) and keratoconus (KC) groups (316 eyes). Tomographic information (Sirius®, Costruzione Strumenti Oftalmici, Italy) was treated with SolidWorks v2013, creating the following morphogeometric parameters: geometric axis-apex line angle (GA-AP), geometric axis-MCT line angle (GA-MCT, apex line-MCT line angle (AP-MCT), and distances between apex and MCT points on the anterior (anterior AP-MCTd) and posterior corneal surface (posterior AP-MCTd). Statistically significant higher values of GA-AP, GA-MCT, AP-MCT and anterior AP-MCTd were found in the keratoconus group (p ≤ 0.001). Moderate significant correlations of corneal aberrations (r ≥ 0.587, p < 0.001) and corneal thickness parameters (r ≤ -0.414, p < 0.001) with GA-AP and AP-MCT were found. Anterior asphericity was found to be significantly correlated with anterior and posterior AP-MCTd (r ≥ 0.430, p < 0.001). Likewise, GA-AP and AP-MCT showed a good diagnostic ability for the detection of keratoconus, with optimal cutoff values of 9.61° (sensitivity 85.5%, specificity 80.3%) and 18.08° (sensitivity 80.5%, specificity 78.7%), respectively. These new morphogeometric indices allow a clinical characterization of the 3-D structural alteration occurring in keratoconus, with less coincidence in the spatial projection of the apex and MCT points of both corneal surfaces. Future studies should confirm the potential impact on the precision of these indices of the variability of posterior corneal surface measurements obtained with Scheimpflug imaging technology.