BACKGROUND During our clinical practice and research, we encountered an interchangeability problem when using the SP-2000P and SP-3000P TopCon corneal specular microscopes (CSMs) (TopCon Medical Systems, Tokyo, Japan) regarding the endothelial cell count (ECC). We describe a method to improve interchangeability between these CSMs. METHODS Five consecutive good-quality endothelial cell photographs were obtained in 22 eyes of 11 subjects. An ECC comparison between the two CSMs was performed after (I) gauging and calibration by the manufacturer, (II) adjustment of the magnification, (III) correction after external horizontal and vertical calibration. RESULTS There was a statistically significant difference between the ECC of the SP-2000P and SP-3000P at the start. The SP-2000P counted an average of 500 cells/mm2 more than the SP-3000P (p=0.00). After correction for magnification and determining a correction factor based on external calibration, the difference between the ECC of the SP-2000P and the SP-3000P was then found to be 0.4 cells/mm2 and was not statistically significant (p=0.98). CONCLUSIONS We propose a method for improving interchangeability, which involves checking magnification settings, re-checking magnification calibration with external calibration devices, and then calculating correction factors. This method can be applied to various specular or confocal microscopes and their associated endothelial cell analysis software packages to be able to keep performing precise endothelial cell counts and to enable comparison of ECCs when a CSM needs to be replaced or when results from different microscopes need to be compared.