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Background Bacterial reinfection of dental cavities remains an unsolved clinical problem. The search for methods enabling the limitation of the bacterial factor has become the fundamental goal of the dental materials research. Silver nanoparticles (AgNPs) are used as disinfection agents. An incomplete polymerization of the polymer resins combined with AgNPs, along with the increase of the release of the unbound monomers, have been found. Objectives The aim of this study was to evaluate the vitality of the human dental pulp stem cells (DPSCs) in response to a disinfection agent containing silver and gold nanoparticles (NPs), different bonding systems, glass-ionomer cement (GIC), and their combinations with the disinfection agent. Also, the influence of these materials both on the secretory function of DPSCs and on their antibacterial properties was established. Material and methods Cytotoxicity (MTT assay) and genotoxicity (enzyme-linked immunosorbent assay - ELISA) assays were used in the study. Antibacterial features were assessed with the optical density (OD) measurement of the bacteria (Streptococcus mutans, Streptococcus salivarius and Lactobacillus acidophilus) kept in dental materials. Results The disinfection liquid proved to be biocompatible. However, it relevantly interfered with the total-etch bonding system in terms of vitality, which may have serious clinical implications. Its combination with the self-etching system was biocompatible, yet it impaired the antibacterial action of the system. An enhancement of antibacterial action of GIC with AgNPs was found. Conclusions The disinfection liquid and GIC were biocompatible toward the DPSCs in terms of cytotoxicity and genotoxicity. Simultaneous usage of AgNPs with other dental materials did not affect the biocompatibility of the used materials. The disinfection liquid and GIC acted as antibacterial agents against all studied bacteria species. Used together with GIC and the total-etch bonding system, the disinfection liquid seemed to be efficient toward bacteria, yet it relevantly impaired the antibacterial action of self-etching systems.