A novel method to locate the centre of keratoconus (KC) and the transition zone between the pathological area and the rest of the corneal tissue is proposed in this study. A spherical coordinate system was used to generate a spherical height map measured relative to the centre of the optimal sphere fit, and normal to the surface. The cone centre was defined as the point with the maximum height. Second derivatives of spherical height were then used to estimate the area of pathology in an iterative process. There was mirror symmetry between cone centre locations in both eyes. The mean distance between cone centre and corneal apex was 1.45 ± 0.25 mm (0.07-2.00), the mean cone height normal to the surface was 37 ± 23 µm (2-129) and 75 ± 45 µm (5-243) in the anterior and posterior surfaces, respectively. There was a significant negative correlation between the cone height and the radius of the sphere of optimal fit (p < 0.05 for both anterior and posterior surfaces). On average, posterior cone height was larger than the corresponding anterior cone height by 37 ± 24 µm (0-158). The novel method proposed can be used to estimate the cone centre and area, and explore the changes in anterior and posterior corneal surfaces that take place with KC progression. It can help improve understanding of keratoconic corneal morphology and assist in developing customized treatments.