Amphibian habitats are easily contaminated by several pollutants, and in agricultural landscapes the likely exposure scenario is represented by pesticides. Many of these substances are known or suspected to act as endocrine disrupting chemicals (EDCs). The goal of the present study was to assess the effects of pyrimethanil, a common-used but also overlooked fungicide, on liver, kidney and gonadal differentiation of Hyla intermedia. Through a multi-organ evaluation, we demonstrated that a long term exposure to two environmentally relevant concentrations of pyrimethanil (5 and 50 µg/L) elicits a range of toxic responses. First we showed that pyrimethanil induces underdevelopment of ovaries and interferes with normal sexual differentiation, thus revealing the endocrine disruption potential of this fungicide. Moreover we revealed that all considered organs are seriously affected by this fungicide and both necrosis and apoptosis contribute to the histological response. This is the first report on the effects of pyrimethanil on gonads, liver and kidney histology of a non-model species and it demonstrates that the hazardous properties of this fungicide can result from several pathological processes affecting different key compartments of amphibian.