To evaluate the direct effect of atrazine (ATZ) and the protective effect of quercetin (QT) on testicular cells, we used primary cultures of rat Sertoli-germ cells (SGCs). ATZ (232 μm) up-regulated the mRNA expression of GATA-4, androgen receptor (AR), androgen-binding protein (ABP), steroidogenic acute regulatory protein (StAR), cytochrome P450 side-chain cleavage enzyme (CYP11A1), cyclooxygenase-2 (COX-2) and NF-κappaB (NF-κB) and down-regulated the expression of stem cell factor (SCF) mRNA. There was no change on the mRNA expression of oestrogen receptor-alpha (ER-α). Simultaneous supplementation of QT in the culture normalizes the expression of these genes. The stimulatory action of follicle stimulating hormone (10 ng/mL) on ATZ-induced StAR and CYP11A1 mRNA levels were also prevented by QT. Furthermore, ATZ-stimulatory action on AR mRNA was opposed in a dose-dependent manner in the presence of increasing concentrations of QT (10–50 μm).The dislodgement of germ cells from the Sertoli cells monolayer and decrease in SGCs viability was prevented by QT. To show whether or not the disrupted interactions of Sertoli and germ cells impaired spermatogenesis, adult male rats exposed in vivo to ATZ (50 mg/kg b.wt) for 1 week had their daily spermatozoa production (DSP) per gram testis lowered by 30%. DSP was significantly increased in the QT(10 mg/kg) + ATZ-treated rats as compared with the ATZ-treated rats. Taken together, ATZ can alter SGCs expression of spermatogenesis- and steroiodogenesis-related genes resulting in a decrease in sperm production in the testis as well as cell viability. QT might block these molecular events-induced by ATZ thereby protecting testicular Sertoli-germ cells from ATZ-induced toxicity.