Morphological studies comparing normal and diseased ear canals use primarily subjective scoring. The aim of this study was to compare normal and severely affected ears in dogs with objective measurements using ImageJ software. Ear canals were harvested from cadavers with normal ears and from dogs that underwent total ear canal ablation for unresolved otitis. Histopathology samples from ear canals were evaluated by semi-quantitative scoring and also by using ImageJ-software for histomorphometric measurements. The normal ears were compared to the severely affected ears using the 2 methods. The 2 methods were significantly (P < 0.0001) correlated for epidermal hyperplasia, ceruminous gland dilation, and hyperplasia and tissue inflammation, which were significantly greater in the severely affected ears (P < 0.0001). This study demonstrated that there is a very high correlation between the 2 methods for the most markedly affected components of otitis externa and that ImageJ software can be efficiently used to measure and evaluate ear canal histomorphometry.