To measure instantaneous velocity fields of venous blood flow in a rat using X-ray particle tracking method. Gold nanoparticles (AuNPs) incorporated chitosan microparticles were applied as biocompatible flow tracers. After intravenous injection of the AuNP-chitosan particles into 7- to 9-week-old male rat vein, X-ray images of particle movement inside the cranial vena cava were consecutively captured. Individual AuNP-chitosan particles in the venous blood flow were clearly observed, and the corresponding velocity vectors were successfully extracted. The measured velocity vectors are in good agreement with the theoretical velocity profile suggested by Casson. This is the first trial to measure blood flow in animals under in vivo conditions with X-ray imaging technique. The results show that X-ray particle tracking technique has a great potential for in vivo measurements of blood flow, which can extend to various biomedical applications related with the diagnosis of circulatory vascular diseases.