The present study was conducted (1) to develop a rapid quantification method of polyhydroxyalkanoates (PHA) concentration in activated sludge by Nile blue A staining and fluorescence measurement and (2) to perform on-line monitoring of PHA concentrations in activated sludge. Activated sludge samples collected from laboratory scale sequencing batch reactors and full-scale wastewater treatment plants were stained with Nile blue A and their fluorescence intensities were determined. There was a high correlation (R2 > 0.97) between the fluorescence intensities of Nile blue A and PHA concentrations in activated sludge determined by gas chromatography. The Nile blue A staining and fluorescence measurement method allows us to determine PHA concentrations in activated sludge within only five minutes and up to 96 samples can be measured at once by using microplate reader. On-line monitoring of PHA concentrations in activated sludge was achieved by using a fluorometer equipped with a flow cell and the time point at which PHA concentration in activated sludge reached the maximum level could be identified. In addition, we examined the influence of pH, floc size and co-existing chemicals in activated sludge suspension on the fluorescence intensities of Nile blue A.