A whole-cell based capacitive biochip (WCB) was employed for detecting nanotoxicity of different types of carbon nanotubes (CNTs). The WCB was made of arrays of capacitors that were functionalized with living S. cerevisiae (yeast) cells through coupling on their cell-surface protein disulfide bridges. Cells-on-chip were exposed to varying concentrations of single-walled (SW), multi-walled (MW) and double-walled (DW) CNTs. Dynamic cell-surface charge distributions as a result of cell-CNT interactions on chip were measured as change in relative capacitance under the applied AC-frequency. The WCB response provided a direct relationship between the integrity of cells-on-chip and their strong interaction with CNTs by adsorption/adhesion. Cellular damages imposed by CNTs was determined based on the magnitude of changes in relative capacitance against different types and concentrations of CNTs. Increasing toxicity experienced by cells-on-chip followed the order DWCNTs < MWCNTs < SWCNTs suggesting that cells were severely affected by SWCNTs followed by MWCNTs and DWCNTs. The above results were further validated through cell viability tests and fluorescence assays using quantum dot conjugated cells that enabled determination of the responses at the interface of cell-membranes against different types of CNTs. The developed WCB can be extended to high-throughput screening of toxic nanomaterials (NMs) in food and environmental samples.