The present invention provides a medical device, preferably a contact lens, which comprises an antimicrobial coating including at least one layer of polyquat of formula (I) or (II). The antimicrobial coating on the medical device of the invention has a high antimicrobial efficacy against microorganisms including Gram-positive and Gram-negative bacterial, a low toxicity, low coefficient of friction, and increased hydrophilicity while maintaining the desired bulk properties such as oxygen permeability and ion permeability of lens material. Such lenses are useful as extended-wear contact lenses. In addition, the invention provides a method for making a medical device, preferably a contact lens, having an antimicrobial coating thereon.