A quantum dot (QD) conjugated whole-cell E. coli biosensor (E. coli-QD bioconjugates) was developed as a new molecular tool for probing cellular damage. The E. coli-QD bioconjugates were viable and exhibited fluorescence emission at 585 nm. Scanning electron microscopy (SEM) analysis of E. coli-QD bioconjugates revealed that the QDs were immobilized on the cell-surfaces and the fluorescence emission from QDs present on cell-surfaces was visualized by confocal microscopic examination. The E. coli-QD bioconjugates were employed as whole-cell fluorescent reporters that were designed to function as fluorescence switches that turn-off when cellular damage occurs. In this study, multi-walled carbon nanotubes (CNTs) were utilized as a model nanomaterial to probe cellular damage. Fluorescence spectra were recorded after the exposure of E. coli-QD bioconjugates with CNTs. We observed a strong correlation between fluorescence emission spectra, SEM and confocal microscopic analysis demonstrating that CNTs induced a dose and exposure time-dependent cellular toxicity. This toxicity mainly occurred by the physical interaction and cellular trafficking mechanisms that led to the collapse of the cellular structure and thus loss of fluorescence. The responses of E. coli-QD bioconjugates against CNTs were also visualized by simply exposing the cells to UV light and therefore rapid toxicity analysis and screening can be made. Our study demonstrated an easy and simple method to determine an important mechanistic perspective for the biological toxicity of chemicals or nanomaterials (NMs).