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To determine the difference between the endothelial cell density (ECD) and the morphologic measurements assessed with a recently developed noncontact specular microscope compared with a contact endothelial microscope. The agreement between the 2 independent operators was also investigated.The central corneal endothelium was examined in the right eyes of 41 healthy individuals using automated image analysis programs without correction for a noncontact specular microscope and a contact specular microscope (EM-3000, EM-1000; Tomey, Tennenlohe, Germany). The evaluated parameters such as ECD, average cell area (AVG), and coefficient of variation of the cell area were determined by 2 operators. Conversion factors were also considered to adjust the ECD values.ECD measurements obtained with the noncontact instrument (2734 ± 287 cells per square millimeter, first operator; 2726 ± 282 cells per square millimeter, second operator) were significantly higher (P < 0.0001) in comparison with the contact microscope (2283 ± 206 cells per square millimeter, first operator; 2274 ± 242 cells per square millimeter, second operator) by both investigators. The contact specular microscope significantly overestimated (P < 0.0001) AVG and coefficient of variation of the cell area values. Statistically significant correlation (P < 0.0001) was detected in ECD (r = 0.77, first operator) and AVG measurements (r = 0.72, first operator) between the 2 endothelial microscopes. Higher degree of agreement between operators was given when using the noncontact specular microscope compared with the contact instrument.The significant differences and the poor agreement between the automated software options disclosed that the 2 instruments cannot be used interchangeably.