N-Trimethyl chitosan chloride (TMC), a chemically modified derivative of chitosan, is the first chitosan derivative shown to be an effective absorption enhancer for peptide and protein drugs across mucosal epithelia. TMC is synthesized by reductive methylation with methyl iodide in the presence of a strong base such as sodium hydroxide. In this reaction, the primary amino group on the C-2 position of chitosan is changed to a quaternary amino group. The charge density, as determined by the degree of quaternization, and probably also the molecular weight of TMC are important factors that influence the absorption enhancement effect and toxicity of this polymer. The molecular weight of the starting polymer decreases during the synthesis procedure due to factors such as the strong alkaline environment and elevated experimental temperatures. This study investigated the effects of two different bases, sodium hydroxide and dimethyl amino pyridine, together with a varying number and duration of reaction steps, on the degradation and the degree of quaternization of TMC polymers. 1H-NMR (nuclear magnetic resonance) spectra showed a major increase in the degree of quaternization (21%-59%) of TMC with an increase in the number of reaction steps when sodium hydroxide was used as the base. Intrinsic viscosity values indicated that the use of dimethyl amino pyridine did not cause polymer degradation to the same extent as sodium hydroxide, but that the degree of quaternization of TMC stayed low (7.3%-9.6%) even when the number of reaction steps was increased. A combination of the two bases did not reduce polymer degradation, while the degree of quaternization was limited to relatively low values (12.5%-34.4%).