The purpose of this study was to improve current methods for the detection of Acanthamoeba spp. in clinical samples. The sensitivity of parasite detection in filtered specimens was evaluated using samples containing different numbers of parasites. They were filtered through cellulose membranes and cultivated on non-nutrient agar plates covered with Escherichia coli. The recovery of amoebae collected by filtration was compared with the cultivation of centrifuged samples. All samples containing 10 parasites per specimen and 65% of samples containing 2 parasites per specimen yielded positive cultures after filtration, while the cultivation results after centrifugation were 8% and 0%, respectively. We conclude that significantly higher sensitivity of parasite detection can be obtained with samples processed by filtration.