Chitosan, a natural polymer obtained by alkaline deacetylation of chitin, is non-toxic, biocompatible, and biodegradable. These properties make chitosan a good candidate for the development of conventional and novel gastrointestinal (GI) drug and gene delivery systems. The objective of this review is to summarize the recent applications of chitosan in oral and/or buccal delivery, stomach-specific drug delivery, intestinal delivery, and colon-specific drug delivery. The use of chitosan for targeting of drugs to each of these sites in the GI tract is illustrated by examples supported by in vivo studies. Chitosan appears to be a promising material for GI drug and gene delivery applications as many derivatives and formulations are being examined.