The recovery rate varied depending on the methods used and test organism. A statistically significant difference in total number of recovered organisms between both recovery methods was found for both T. pyriformis and A. castellanii. T. pyriformis was recovered in significantly higher numbers with the centrifugation method than with the stomacher protocol (p < 0.001), whereas for A. castellanii, significantly higher numbers were counted after usage of the stomacher method in comparison with the centrifugation protocol (p < 0.001). For the flagellate Cercomonas sp., no statistically significant differences between both recovery protocols were found.