Aims and objectives: Jatropha is a medicinal plant that has anti-inflammatory properties. This plant is being developed as a male contraceptive drug, especially for densely populated areas. Jatropha seeds contain a toxic compound in the form of currant. This compound is thought to be able to affect the male reproductive organs by inhibiting sperm production and reproductive hormones. So, this study aims to determine the histological structure of male rat testes after being given Jatropha seed extract. Materials and methods: This research is an experimental design. There were five doses of Jatropha seed extract treatment, which were given every day for 28 days. Each treatment group contained five male rats. Observations were made on the testes with hematoxylin and eosin (HE) staining. Parameters were measured by measuring the length of the diameter of seminiferous tubules, counting Leydig cells and primary spermatocytes. Results: Histological data of testicular organs after being given Jatropha seed extract (doses 0, 5, 25, 50, and 250 mg/kg BW) were obtained—seminiferous tubule diameter 1040, 847, 869, 1005, and 842 μm; the number of Leydig cells is 36, 121, 85, 40, and 63; and primary spermatocyte counts showed 152, 205, 122, 143, and 138 [analysis of variance (ANOVA); p < 0.05]. The seminiferous tubule and Leydig cell counts both positively correlated with primary spermatocytes. Conclusion: Jatropha seed extract has potential in the development of male contraception, as evidenced by the seminiferous tubules as sperm producers having a smaller diameter and a reduced number of primary spermatocytes. The increase in Leydig cells indicates the testosterone hormone is formed, the process of spermatogenesis continues, and continues to influence the male secondary sex characteristics. Research highlights: This study found that there was a narrowing of the seminiferous tubule diameters in the administration of Jatropha seed extract compared to the control group, indicating a change in the structure of the organ. This study found Leydig cells increased compared to the control; this shows testosterone production is not disturbed. Primary spermatocyte cell count decreased compared to control, indicating decreased spermatozoa production. The three research parameters are seminiferous tubule diameter, number of Leydig cells, and primary spermatocytes after being given Jatropha seed extract. This information is expected to be used as a basis for the development of male contraceptive drugs.