Exposure of fathead minnow (Pimephales promelas), Japanese medaka (Oryzias latipes) and zebrafish (Danio rerio) to endocrine disrupting chemicals may result in histopathological alterations of gonadal structure and microarchitecture. The diagnosis of such histopathological changes may, therefore, assist in the detection of endocrine disrupting chemicals. Given the long historical background of piscine histopathology and diverse traditions in the terminology in different fish species and in different regions, there is a need for harmonisation in order to facilitate non-biased comparisons of results from different laboratories and, thus, to optimise reproducibility and reliability of histopathological diagnoses. The purpose of this document is to provide guidance for the preparation and histopathological evaluation of gonads from fathead minnow, Japanese medaka and zebrafish following exposure to chemicals potentially disrupting the endocrine system.