The widely used herbicide atrazine is a potent endocrine disruptor known to cause increased aromatase expression and transient increase in testicular weight followed by remarkable testis atrophy. However, whether the effects of atrazine on the testes are primary or secondary to dysfunctions in other components of male reproductive tract remains unknown. Given the high sensitivity of the efferent ductules to estrogen imbalance and the similarity to alterations previously described for other disruptors of these ductules function, and the testicular alterations observed after atrazine exposure, we hypothesized that the efferent ductules could be a target for atrazine. Herein we characterized the efferent ductules and the ventral prostate of adult Wistar rats treated with 200 mg/kg/day of atrazine for 7, 15, and 40 days. Additionally, we evaluated if the effects of atrazine in these organs could be reduced after discontinuation of the treatment. Atrazine exposure resulted in mild effects on the ventral prostate, but remarkable alterations on the efferent ductules, including luminal dilation, reduced epithelial height, and disruption of the epithelial homeostasis, which coincides with increased aromatase expression. Together with our previous data, these results suggest that at least part of the testicular effects of atrazine may be secondary to the alterations in the efferent ductules.