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The use of energy dispersive analysis of X-rays (EDAX) to identify and quantify the presence of chlorhexidine diacetate (CHA) within Saccharomyces cerevisiae cells was examined. Chlorine was used as the elemental marker tag. Saccharomyces cerevisiae cells exposed to 1000 μg ml-1 CHA took up increasing amounts of CHA over a time period of 30 s to 30 min. Electron probe micro-analysis was employed to examine the specific accumulation of CHA across the treated cells. These results showed that CHA was distributed evenly between the cell wall, cytoplasm and vacuoles of cells pre-treated with this concentration of CHA for 30 min. The EDAX system therefore provides a useful tool for examining the qualitative and quantitative effects of chlorhexidine on yeast cells, although quantitative data must be interpreted with caution.