Carboxymethyl chitosan (CM-chitosan) is one of water-soluble derivatives of chitosan. Numerous studies have been focused on its applications as pharmaceutical excipient, bioactive reagent and nontoxic drug carrier. Like other polysaccharides, CM-chitosan is inhomogenous in molecular weight. Originations and preparation procedures considerably influence its molecular weight and molecular weight distributions. Understanding the molecular weight related biological behaviour of this inhomogenous glycopolymer in vivo were crucial for the quality control and clinical applications of chitosan and chitosan based medical devices. In this study, we investigated the effects of molecular weights on the absorption, distribution, degradation and urinary excretion of the fluorescein isothiocyanate-labeled CM-chitosan in rats. The results indicated that molecular weight significantly influenced the uptake of CM-chitosan from the lumen of abdomen and blood vessels to peripheral tissues, the distribution of this chemical and urinary excretion after intraperitoneal administration. These findings provided an important reference for the clinical applications of this versatile derivative of chitosan as postsurgical and other biomedical materials and important clues for the exploitation of CM-chitosan based drug targeting and delivery systems.