Chitosan is a natural polysaccharide which is generally biodegradable, biocompatible and mucoadhesive, thus, attracting considerable interest of scientific researchers. The application of chitosan as nanocarriers for drug delivery thrived. And some of their pharmacokinetics and biodistribution profiles were studied, which are crucial to develop a promising drug delivery system. In this article, we will first give an introduction for the chitosan as drug delivery system, especially as nanoparticles. Then, we focus on pharmacokinetics studies of various chitosan nanoparticles both in vitro and in vivo. In a following part, we refer to researches on biodistribution properties of chitosan nanoparticles. Here we crucially discuss the in vivo fate of chitosan nanoparticles. And finally, toxicity issue is discussed and conclusions are drawn.