Confocal microscopy allows high-resolution in vivo imaging of corneal endothelial cells and potentially offers advantages over specular microscopy, the current ‘gold-standard’ technique. The purpose of our study was to determine if corneal confocal microscopy and non-contact specular microscopy are clinically comparable methods for assessing corneal endothelial morphometry in vivo. The corneal endothelium was examined quantitatively in 50 healthy eyes using a noncontact specular microscope (SP-1000, Topcon Corp., Tokyo, Japan) and a corneal confocal microscope (ConfoScan 3, Nidek, Italy). In addition, the corneal endothelium of a subject with reduced corneal transparency (due to Fuchs’ endothelial dystrophy) was examined using both instruments. There was relatively good agreement between the two instruments for the indices of polymegethism and pleomorphism. When assessing endothelial cell density (ECD), the values obtained with the ConfoScan 3 confocal microscope were consistently lower than those obtained with the SP1000 specular microscope. The confocal microscope provided superior-quality images in the subject with corneal oedema due to Fuchs’ endothelial dystrophy. In conclusion, both non-contact specular microscopy and corneal confocal microscopy are viable methods for assessing endothelial morphometry in the living human cornea, although the values obtained are not directly interchangeable. Confocal microscopy offers advantages over specular microscopy for endothelial imaging when corneal transparency is reduced due to moderate levels of corneal oedema.