Safety testing of nanoparticles (NPs) relies on robust, predictive, and reproducible methods. Integrated test strategies usually start with the assessment of in vitro cytotoxicity. Methods for this purpose are only partially established for NPs. The aim of this study was to evaluate three cytotoxicity assays for their applicability to NPs in several human cell models representing the most important NP target organs and to compare cell responses. The assays covered different biological principles, i.e. ATP content, redox metabolism, and membrane permeability, as well as different read-out principles, i.e. luminescence, colorimetry, and fluorescence. For all assays standard operating procedures were developed. A549 and NCI-H441 lung epithelial cells in single and in co-culture with THP-1 derived macrophages served as lung epithelial models. Normal human epidermal keratinocytes and in vitro reconstituted human epidermis were employed as skin models. Undifferentiated and differentiated Caco-2 gut epithelial cells were applied as gut epithelial models. Primary CD34-derived dendritic cells (CD34-DCs) served as an immune model. We used well-characterized model NPs, i.e. 50 nm amine-modified and 50 nm carboxyl-modified polystyrene NPs (PS-NH2 and PS-COOH, respectively). PS-COOH NPs showed no effect in any test while PS-NH2 displayed cytotoxicity in most cell models. CD34-DCs was the most sensitive cell model tested. The tetrazolium-based MTS assay was the most robust assay in our study, applicable to all cell models investigated. Therefore, this assay could become an integral part of a NP testing strategy. Other assays might be also useful, depending on the cell model or the type of investigation.