The field of carbon nanotube (CNT) functionalisation is increasingly growing for the purpose of enhancing the biocompatibility of CNT for medical and biological applications. Properties of CNT such as the type of functionalisation, charge density, and the dispersibility profile are expected to modulate CNT cellular uptake and toxicity profile in vitro. The assay described here allows for rapid screening of CNT cellular uptake in vitro and assessing the acute cytotoxicity simultaneously. CNT cellular uptake is measured qualitatively by light scattering analysis without differentiating between cell binding and internalisation of the CNT by the cells. In addition, flow cytometry is used to combine light scattering analysis with flow cytometry-based Annexin V/propidium iodide assay to measure the cytotoxicity. This assay is rapid, reliable, and allows for comparative analysis between various types of CNT studied.