Chitosan, a natural-based polymer obtained by alkaline deacetylation of chitin, is nontoxic, biocompatible, and biodegradable. These properties make chitosan a good candidate for conventional and novel drug delivery systems. This article reviews the approaches aimed to associate bioactive molecules to chitosan in the form of colloidal structures and analyzes the evidence of their efficacy in improving the transport of the associated molecule through mucosae and epithelia. Chitosan forms colloidal particles and entraps bioactive molecules through a number of mechanisms, including chemical crosslinking, ionic crosslinking, and ionic complexation. A possible alternative of chitosan by the chemical modification also has been useful for the association of bioactive molecules to polymer and controlling the drug release profile. Because of the high affinity of chitosan for cell membranes, it has been used as a coating agent for liposome formulations. This review also examines the advances in the application of chitosan and its derivatives to nonviral gene delivery and gives an overview of transfection studies that use chitosan as a transfection agent. From the studies reviewed, we concluded that chitosan and its derivatives are promising materials for controlled drug and nonviral gene delivery.