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Polyelectrolyte complexes (PEC) formed between chitosan derivatives and enoxaparin were prepared by a self-assembly process and were characterized in terms of particle size and surface charge. The morphology was observed by atomic force microscopy (AFM). The colloidal stability and bioadhesion of the PEC were characterized by dynamic light scattering (DLS). The absorption of enoxaparin in rats was evaluated by activated partial thromboplastin time (APTT) assay. It was shown that the prepared PEC had a spherical shape with positive charge and a mean diameter in the range of 200–600 nm. An increase in temperature led to a decrease in particle size (ca. 10%) with an increased kcps value (ca. 10–20%) for the PEC studied, depending on the polymer structure. Thiolation and methylation of chitosan could significantly improve the corresponding PEC's bioadhesion and hence the oral absorption of enoxaparin. A good relationship between bioadhesion and in vivo absorption was established. However, PEC of PEGylated chitosan did not display a significantly enhanced permeation of enoxaparin compared with unmodified chitosan. In conclusion, the oral bioavailability of enoxaparin can be enhanced by improving the bioadhesive properties of PEC via the chemical modification of chitosan employed.