Blastocystis is a common intestinal parasite that can inhabit the intestinal tract of humans and many animals. Despite it was firstly described almost 100 years ago; many subjects are still under debate about Blastocystis, including its life-cycle, pathogenic potential and treatment of infected individuals. Historically, local plant species have been used for therapeutic purposes by the local people of Anatolia. Here, hexane and methanol extracts of two local plants, Quercus infectoria (Fagaceae) and Achillea millefolium, which have been used against diarrhea in Anatolia, were examined for their in vitro efficacies against Blastocystis. LC50 and EC50 values of the plant extracts were determined by Brine Shrimp and Graphpad Prism 5 (R) methods, respectively. The results showed that LC50 (500 mu g/ml) and EC50 (198.8 mu g/ml) concentrations of the methanol extract of A. millefolium were lowest compared to other extracts, its anti-Blastocystis activity was found to be comparable to metronidazole and it showed no cytotoxic activity. These initial results suggest that the methanol extract of A. millefolium may be a novel option for the treatment of Blastocystis infections in humans in future, if confirmed by further, larger-scale studies.