Although fenarimol is a widely used chlorinated fungicide applied to fruits and vegetables and considered as a suspected endocrine disrupter (ED), transgeneration studies of fenarimol at its low doses are not available. Objectives: The aims of this study are to address the effect of perinatal exposure to low doses of fenarimol on reproductive performance and to investigate molecular and cellular mechanisms which are associated with. Methods: The body and organ weights and anogenital distance (AGD) of mice offspring (F1) maternally exposed to fenarimol were determined, and their reproductive performances were assessed by mating and ovarian follicular and sperm analyses. In addition, differentially expressed genes (DEGs) in F1 ovaries were identified by DNA microarray. Up-regulated genes were confirmed by quantitative real-time PCR (qRT-PCR) and immunohistochemical analysis. Results: Fenarimol-exposed F1 mice showed the shortened AGD, increased body weight with altered organ weights, increased number of pub, abundant follicles, and enhanced sperm count and quality. Microarray data showed 82 up-regulated and 742 down-regulated genes on the ovaries of fenarimol-exposed mice, in which Cyp17a1 and Cyp19a1 were up-regulated. Conclusions: Low doses of perinatal fenarimol exposure caused reproductive dysfunction in mice and thus can possibly impose risks on reproductive activities of human and wild-life.