Red blood cells (RBC) become deformed while flowing through capillaries. We captured images of blood flow in capillaries and of RBC in the rat mesentery using a high-speed camera at 2000 frames/s and then directly measured and estimated the deformation and velocity of RBC in a non-uniform capillary. The distribution of the capillary diameter was determined by image processing. We applied a deformation index and simple modeling to observe RBC deformation in capillaries. The average capillary diameter was approximately 6.2 microm, and the average velocity of RBC was about 1.85 mm/s. The average deformation index of RBC in the capillary was about 1.55. The present results showed that RBC in capillaries generally assume a specific shape depending on external forces such as the velocity of the blood flow and capillary diameter in vivo.