Background & aim: Conazoles including imidazoles or triazoles are anti- fungal agents widely used to prevent fungal growth and their infections. Propiconazole placed in this group is a systemic fungicide used widely for detoxification of cereal seeds especially rice in Iran and other countries. This fungicide were designed to inhibit a specific cytochrome P450, CYP51 (lanosterol-14-α- demethylase), a critical step in the biosynthesis of ergosterol, a steroid required for the formation of the fungal cell wall. In the present experimental study, the effect of propiconazole on Caspase 9 gene expression profile as an initiator of apoptotic process and protective effect of selenium were investigated. Methods: Forty SD rats were divided into 10 groups of 4,  including : control , sham1 (solvent of propiconazole, distilled water), sham 2 (solvent of selenium, normal saline) and 1 group received 0.5 mg/kg selenium ,3 groups received propiconazole in doses of 10,50,75  mg/kg and 3 groups received propiconazole in doses of 10,50,75 mg/kg propiconazole with 0.5 mg/kg of selenium. Injections were intrapritoneal for two weeks in alternate days. Then, using RT-PCR and Total Lab program gene expression of caspase-9 testicular of all groups were studied. Data were analyzed using descriptive statistics. Results:  A significant increase of caspase 9 expression were observed among all experimental groups compared to control and sham groups. These findings indicated that 0.5 mg/kg selenium is not a suitable dose to create protection in this experimental study.  Conclusion: The significant increase in Caspase 9 gene expression profile observed in all experimental groups as compared to control suggests activation of apoptosis and inefficacy of selenium to protect the testis against induced damages.