Structural changes in the lamina cribrosa have been implicated in the pathogenesis of glaucomatous optic atrophy. The aim of this study was to determine a measure the surface variability of the cup floor in normal subjects and patients with glaucoma.A sample of age matched normal subjects (NN), patients with low tension glaucoma (LTG), and primary open angle glaucoma (POAG) were included in the study. The glaucoma groups were matched for the severity of the visual field loss. Mean 10 degree topographic images of normal and glaucomatous eyes from the Heidelberg retina tomograph were imported into ERDAS image processing software where topographic analysis of the cup floor could be assessed. Each image was processed using customised spatial filters that calculated the surface depth variation in localised neighbourhood areas across each image. The local change in depth across the cup floor surface was determined and compared between the three clinical groups.The depth variation in the cup floor was largest in normal subjects followed by LTG and POAG. Highly statistically significant differences in surface depth variability of the cup floor existed between normal and LTG (p = 0.005), between normal and POAG (p<0.0001), and between LTG and POAG groups (p<0.0001). The variability and skewness of depth difference across the optic cup floor were also significantly different between the three clinical groups.A new parameter quantifying depth variations in the cup floor significantly discriminated between groups of normal and glaucoma patients. This new parameter may contribute to a better understanding of the pathogenesis of the glaucomatous optic nerve damage in different types of glaucoma.