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The aim of this study was to overcome the analytical problems encountered during the detection of protozoans by flow cytometry resulting from particle compaction.Malvern Mastersizer (Malvern Instruments, Malvern, UK) was used to characterize the particle distribution of four different water samples and/or particle concentrates incubated with (i) low ionic strength solution or sequestring agent, (ii) anionic or non-ionic surfactants (iii) industry detergent formulations and (iv) physical treatment. The recovery of oocysts and cysts in seeded and treated particle concentrates was estimated by cytometry and microscopy. The decrease in ionic strength of the aqueous solution was most efficient in particle dispersion for different types of water. Moreover, samples treated with deionized water or tetrasodium pyrophosphate showed the highest recovery with more than 80% of the oocysts and cysts recovered.Chemical treatments that act by altering the ionic strength of the medium are the most efficient for all water types tested here but the overall detergency performance cannot be predicted for all water types.Flow cytometric detection has been replaced largely by immunomagnetic separation but the data recorded still have relevance in this technique as well as in molecular techniques requiring DNA or RNA extraction.