The transmucosal routes such as pulmonary, nasal and oral routes are most important and common routes for drug delivering to the body. However, peptide and protein drugs are degraded before they reach the blood stream and cannot cross the mucosal barriers. The mucoadhesive polymer-coated nanoparticles colloidal carriers can solve these problems. In the present investigation, mucoadhesive polymer-coated nanoparticles were prepared by emulsion polymerization process. A detailed preparation procedure of the mucoadhesive polymer-coated nanoparticles was provided. The parameters such as portion of the mucoadhesive polymers and concentration of the radical initiator were investigated. The resulting chitosan-coated nanoparticles colloids possessed positive surface charge, while poly(acrylic acid)-coated nanoparticles colloids and carbopol-coated nanoparticles colloids had negative surface charge. These nanoparticles were suitable for carrying hydrophilic protein or peptide drugs. Chitosan-coated nanoparticles were stable when pH value below 11, while poly(acrylic acid)-coated nanoparticles and carbopol-coated nanoparticles were stable under physiological pH conditions. Therefore, they are promising for transmucosal drug delivery.