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We report different mesoporosity-dependent and functional group-dependent cytotoxicity and endocytosis of various silica nanomaterials on suspended and adherent cells. This dependency further varied with incubation time and particle dosage, and appeared to be associated with the particles’ endocytotic efficiency and their chemical and physical properties. We studied two common mesoporous nanomaterials (MSNs), MCM-41 and SBA-15, and one type of solid-cored silica microsphere, paralleled by their quaternary amine functionalized counterparts. Compared to SBA-15, MCM-41 has a larger surface area but smaller pore size, whereas SMS exhibits low surface area and poor porosity. In Jurkat cells, SBA-15 and MCM-41 exhibited different cytotoxicity profiles. However, no significant cell death was detected when treated with the aminated MSNs, indicating that the positively charged quaternary amines …