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Several therapeutic effects have been reported for Peganum harmala and Piper longum. These plants contain flavonoids that probably can affect reproductive endocrine system and reduce fertility. In this study, the impacts of hydroalcoholic extracts of Peganum harmala and Piper longum on pituitary-gonadal axis were investigated. Male mice were divided into one control group and three experimental groups. The first experimental group received the extract of Peganum harmala (200 mg/lit), while the second experimental group received the extract of Piper longum (200 mg/lit) and the third experimental group received the combination of both extracts (200 mg/lit) for 30 days. After the treatment, spermatogonia, spermatocytes and spermatids were counted and serum levels of testosterone, follicle-stimulating hormone (FSH), and luteinizing hormone (LH) were measured. Data were analyzed by SPSS software. Levels of testosterone, FSH and LH showed a significant decrease in the first and third experimental groups in comparison with the control group. Moreover, the number of spermatogonia, spermatocyte and spermatid decreased in these groups. The results of the present study demonstrated that hydroalcoholic extract of Peganum harmala and Piper longum can decrease the pituitary gonadal axis function and spermatogenesis in male NMRI mice.