Fourier analysis of in vivo human corneal endothelial cell structure was investigated using specular photomicrographs for a range of ages from less than one year to over 70. The theoretical basis for this analysis was investigated using mathematical models of cell structures where the elements determining their form could be modified in a controlled and quantified manner. The resulting Fourier transform properties were related to properties of cell structure. The experimental factors underlying this analysis were then studied using digitized images of corneal endothelial cells. It was found that the Fourier transforms provided quantitative descriptions of population cell size and organisation. For the smaller, more regular cell structure from the younger eyes, the expected larger rings of the Fourier transforms were demonstrated. Specular photomicrographs of older eyes gave rise to smaller diameter rings in their Fourier transforms. These results are consistent with the previous studies which used manual tracings of human endothelial cell patterns. This is the first demonstration of the direct Fourier analysis of clinical human corneal specular photomicrographs.