Antimicrobial nanogels, aggregates, and films are prepared by complexation of the antiseptic and bacteriostatic agent chlorhexidine (CHX) for medical and dental applications. A series of α-, β-, and γ-cyclodextrin methacrylate (CD-MA) containing hydrophobic poly(methyl methacrylate) (PMMA) based nanogels are loaded quantitatively with CHX in aqueous dispersion. The results show that CHX is enhancedly complexed by the use of CD-MA domains in the particles structure. β-CD-MA nanogels present the highest uptake of CHX. Furthermore, it is observed that the uptake of CHX in nanogels is influenced by the hydrophobic PMMA structure. CHX acts as external cross-linker of nanogels by formation of 1:2 (CHX:CD-MA) inclusion complexes of two β-CD-MA units on the surfaces of two different nanogels. The nanogels adsorb easily onto glass surfaces by physical self-bonding and formation of a dense crosslinked nanogel film. Biological tests of the applied CHX nanogels with regard to antimicrobial efficiency are successfully performed against Staphylococcus aureus.