The success of gene therapy is dependent on finding effective carrier systems. Viral vectors have been widely used in vivo and in clinical trials due to their high transfection efficiency; however, they have several disadvantages, including immunogenicity, potential infectivity, inflammation, and complicated production. Therefore, non-viral vectors have recently been tried as an alternative. Among non-viral vectors, chitosan and chitosan derivatives have been investigated due to several advantages, including biocompatibility, biodegradability, and low toxicity. However, the low transfection efficiency of DNA (or low gene silencing of siRNA) and the low cell specificity of chitosan as a gene carrier need to be overcome before clinical trials. The objective of this review is to discuss the use of chitosan and chitosan derivatives in gene therapy, and the effect of several parameters on transfection efficiency of DNA (or gene silencing of siRNA). Also, specific ligand and pH-sensitive modifications of chitosan for improvement of cell specificity and transfection efficiency (or gene silencing) are explained.