The cellular toxicity of three types of carbon nanoparticles, namely HiPco single-walled carbon nanotubes (SWCNT), arc discharge SWCNT and Printex 90 carbon black nanoparticles, was studied on three different cell models including the human alveolar carcinoma epithelial cell line (A549), the normal human bronchial epithelial cell line (BEAS-2B) and the human keratinocyte cell line (HaCaT) using the clonogenic assay. Carbon nanomaterials are known to interact with colorimetric indicator dyes frequently used in cytotoxicity assays. By employing the clonogenic assay, any such interactions could be avoided, allowing a more reliable method for the in vitro toxicity assessment of carbon-based nanoparticles. It could be shown that the toxicity of as produced SWCNT samples differs between cell lines and the SWCNT production method used, with HiPco SWCNT samples being more reactive compared to arc discharge produced SWCNT samples, both eliciting a stronger cytotoxic response than carbon black. Furthermore, it was possible to distinguish between effects on cell viability and cell proliferation by including colony size as an additional endpoint in the clonogenic assay. All three particle types were highly effective in inhibiting cell proliferation in all three cell lines, whereas only HaCaT and BEAS-2B cells also showed decreased cell viability.