Glass ionomer cements (GICs) are commonly used for cementing full cast crown restorations. Regrettably, although the dental cements fill the gap between the tooth and the crown, bacterial microleakage may occur, resulting in secondary caries. As microleakage cannot be completely prevented, GICs possessing antibacterial properties are in demand. In the present study the antibacterial activity of insoluble, cross-linked quaternary ammonium polyethylenimine (QPEI) nanoparticles incorporated at 1% w/w in two clinically available GICs were studied. The antibacterial activity was tested against Streptococcus mutans and Lactobacillus casei using the direct contact test (DCT) and the agar diffusion test (ADT). Using the direct contact test, antibacterial activity (P<0.05) was found in both tested GICs with incorporated QPEI nanoparticles, the effect lasting for at least one month. However, the ADT showed no inhibition halo in the test bacteria, indicating that the antimicrobial nanoparticles do not diffuse into the agar. The results show that the incorporation of QPEI nanoparticles in glass ionomer cements has a long-lasting antibacterial effect against Streptococcus mutans and Lactobacillus casei. Changing the antibacterial properties of glass ionomer cements by incorporating QPEI antibacterial nanoparticles may prolong the clinical performance of dental crowns.