In this study, three methods commercialized by Pall (Envirochek HV), Idexx (FiltaMax) and Whatman (Cryptest) to concentrate Giardia cysts and Cryptosporidium oocysts from surface and drinking waters were compared according to the EPA standard protocol. Twenty litres of surface and 100 litres of drinking waters were inoculated with 10(3) (oo)cysts before being concentrated by filtration. Our results show that recovery rates of Giardia cysts from surface water was significantly higher using FiltaMax (91+/-12%) than Cryptest (57+/-9%) or Envirochek HV (60+/-4%) while recovery from drinking water was equivalent using FiltaMax (84+/-7%) or Cryptest (78+/-7%) but lower using Envirochek HV (34+/-29%). Recovery of Cryptosporidium oocysts from surface water was significantly higher using Envirochek HV (65+/-5%) than using FiltaMax (45+/-7%) or Cryptest (50+/-7%) while recovery rates from drinking water was equivalent using either FiltaMax (48+/-8%), Cryptest (57+/-4%) or Envirochek HV (64+/-22%). Finally, regardless of the water type, all methods tested allowed recovery rates superior to 24% complying with the EPA standard protocol. Timing, material and practicability associated with each method are discussed.