This review considers the application of chitosan and its salts in the delivery of drugs intended to act locally towards diseases of the mucosa itself (mucosal delivery), and to undergo systemic absorption by means of transmucosal routes (transmucosal delivery). Those chitosan properties that are particularly useful in mucosal and transmucosal delivery have been reviewed, such as mucoadhesion, penetration enhancement and peptidase inhibition behaviour. Chitosan bioactive properties have also been considered, such as anti-infective, haemostatic, wound healing and immune-stimulating activity. Chitosan is available with a wide range of molecular mass and deacetylation degree: the influence of these properties on polymer performance and solubility has been taken into account. As solubility in particular can strongly limit the results obtained at pH values close to neutrality, particular attention has been paid to chitosan salts and derivatives with modified solubility. Thanks to the presence of positively charged amino groups of the polymer, a subject of increasing interest is the exploitation of its interaction with acidic molecules having potential synergistic behaviour towards bioactive properties, or even with acidic drugs. The aim of the review is to describe not only some properties of chitosan, but also the way they can be modified by the acidic moiety.