Background;: Leishmaniasis is one of the major diseases caused by the intracellular parasite of Leishmania. It has become one of the most dangerous health problems today. Our aim of the present study is to compare the effects of Sambucus ebulus leaf and fruit extracts on Leishmania major in vitro. Methods: In this study, we used MTT, promastigote and amastigote assay to evaluate the effect of different concentrations of the extract on parasite and we compared their effects. The flow cytometry technique was also used to detect the apoptotic effect of the extracts on promastigotes. Results: According to MTT experiment IC50 concentration of leaf and fruit extracts on parasite was 157 μg/ml and 265 μg/ml, respectively. After analysis by flow cytometry, leaf and fruit extracts also showed apoptosis effect. Leaf and fruit extract caused 40.2 and 2.67 percent apoptosis. Conclusion: Based on the above assessment, we determined that the S. ebulus leaf extract has a more toxic effect on promastigotes and amstigotes than its fruit extract and maybe in the future that be used as a drug candidate.