Some studies show the uptake of disinfectants on medical devices but no studies on their cytotoxicity have been reported. This study aimed to assess that cytotoxicity in a 3-dimensional culture system using HeLa cells grown in matrices composed of collagen. Plastic materials were soaked in the use solutions of the widely used high-level disinfectants, glutaraldehyde (GA), ortho-phthalaldehyde (OPA) and peracetic acid (PAA). After being rinsed, they were allowed to dry and were embedded into the cell medium to investigate the cytotoxicity of the residual disinfectants. Cytotoxicity was observed with the polyvinyl chloride, polyurethane and silicon tubes soaked in GA and OPA, indicating that both disinfectants were absorbed in the test pieces, whereas for PAA, none was observed. As for the polytetrafluoroethylene (PTFE) tubes, no disinfectant displayed cytotoxicity. GA and OPA are primary irritants, having a potential to cause anaphylaxis and other forms of allergic reactions. There should be consideration not only about the toxicity of the residual disinfectant from poor rinsing, but also about the toxicity that would result from the disinfectants that were absorbed and consequently released from the medical devices or materials.