Giardiasis is endemic in Iran and metronidazole and furazolidone are used for its treatment. The drugs have some adverse effects. Herbal medicine is a novel area for new drugs. Various concentration of essential oil, boiled and aqueous Soxhlet extracts of Thymus vulgaris compared with metronidazole on Giardia lamblia cyst in 30 and 60 minutes. The undiluted concentration of essential oil of the plant had the most lethal effect (91.1 %; max, 97.8%, min, 77.8%) in comparison to metronidazole (89.4%, max, 95.6%, min, 83.3%), boiled extract of the plant (7%, max, 20, min, 0%) and aqueous Soxhlet extract of the plant (13.8%, max, 22%, min, 8%) in 60 minutes. Thus, essential oil extract of Thymus vulgaris can be a suitable substitute to metronidazole in giardiasis, however, clinical trials should be planned to prove this recommendation.