To overcome the limitations of the conventional inhibition method for mechanism study, here we developed a combined CLSM technique as an alternative approach to evaluate and explain the antibacterial process of nanostructure at single cell level. Three different nanostructures (dumbbell-shaped ZnO, rod-shaped ZnO and ZnO/Ag composites) were examined here as a model system. Their antibacterial processes against Escherichia coli (E. coli) were quantitatively studied in detail. According to the obtained time-dependent mean fluorescence intensity (MFI) decay dynamics, an interesting two-step cellular disruption process was observed and discussed for the first time. The combined CLSM technique described here is superior to standard growth method for they can provide a more detailed and reliable description of cell-nanostructure interactions. (C) 2012 Elsevier B.V. All rights reserved.