Here, we supplied a direct and rapid quantum dots labelling method of bacterial cells in food, water and environmental contaminations. Outer layers of Escherichia coli cells prevent cells from direct interactions with molecules and objects such as quantum dots. Permeabilization treatment of E. coil cells may facilitate macromolecules penetrate cell walls and improve internal bacterial quantum dots (QDs) labelling. In this work, we investigated direct internal QDs labelling of E. coli cells permeabilized using three methods including chloroform-SDS treatment, lysozyme-EDTA treatment and osmotic shock treatment. Effects of permeabilization were analysed by scanning electronic microscopy and measuring activity of alkaline phosphatase (PhoA) released from periplasm. Internal bacterial QDs labelling was monitored by flow cytometry and fluorescent microscopy. After chloroform-SDS or lysozyme-EDTA treatment, cells could be directly labelled with QDs. No interaction was observed between osmotic shock treated cells and QDs. The mechanism of cell permeabilization explaining different labelling efficiency has been established. The QDs labelling approach presented in this work provides a simple, rapid and sensitive detection method for multiple purpose bacterial analysis in combination with biological techniques. (C) 2012 Elsevier Inc. All rights reserved.