Ultrasonographic morphometry of wall layers is commonly used in veterinary patients with suspected small intestinal disease, however published studies comparing this method with histopathology in horses are limited. This prospective, methods comparison study compared the qualitative and quantitative characteristics of small intestinal wall layers using ex vivo high-frequency ultrasound versus histopathology in a sample of 16 horses. Transverse section images of duodenum, distal jejunum, and ileum were acquired with a high-frequency linear transducer (7-15 MHz). Transverse histological cryosections were obtained at the same level. Appearance and measurements of the intestinal wall layers were assessed on the ultrasonographic and histological images.High-frequency scanning with the probe in close contact with the serosal surface of the equine intestinal wall allowed a clear and detailed definition of wall layers. A hyperechoic line was consistently detected within the tunica muscularis in all the intestinal tracts, corresponding histologically to the interface between its longitudinal and circular muscle layers. The overall trend of the values for wall layers thickness was comparable between ex vivo ultrasonography and histology. However, a poor agreement was found between the two methods for all layers. The ultrasonographic measurements were thicker compared to histological measurements, with the exception of the total wall and the muscular layer thicknesses. These layers were thinner on ultrasonography in the duodenum and in all the intestinal segments, respectively. Findings from the current study can be used as background for future ultrasonographic investigations of small intestinal diseases in horses.