Microorganisms growing on painted surfaces are not only an aesthetic problem, but also actively contribute to the weathering and deterioration of materials. A widely used strategy to combat microbial colonization is the addition of biocides to the paint. However, ecotoxic, non-degradable biocides with a broad protection range are now prohibited in Europe, so the paint industry is considering engineered nanoparticles (ENPs) as an alternative biocide. There is concern that ENPs in paint might be released in run-off water and subsequently consumed by animals and/or humans, potentially coming into contact with cells of the gastrointestinal tract and affecting the immune system. Therefore, in the present study we evaluated the cytotoxic effects of three ENPs (nanosilver, nanotitanium dioxide and nanosilicon dioxide) that have a realistic potential for use in paints in the near future. When exposed to nanotitanium dioxide and nanosilicon dioxide in concentrations up to 243 µg/mL for 48 h, neither the gastrointestinal cells (CaCo-2) nor immune system cells (Jurkat) were significantly affected. However, when exposed to nanosilver, several cell parameters were affected, but far less than by silver ions used as a control. No differences in cytotoxicity were observed when cells were exposed to ENP-containing paint particles, compared with the same paint particles without ENPs. Paint particles containing ENPs did not affect cell morphology, the release of reactive oxygen species or cytokines, cell activity or cell death in a different manner to the same paint particles without ENPs. The results suggest that paints doped with ENPs do not pose an additional acute health hazard for humans.