Water pollution induces pathological changes in fish. As an indicator of exposure to contaminants, histology represents a useful tool to assess the degree of pollution, particularly for sub-lethal and chronic effects. However, a standardized method for the description and assessment of histological changes, mainly for use in freshwater fish, is still lacking. In this paper, the present authors propose a standardized tool for the assessment of histological findings which can be applied to different organs. The methodology is based on two factors: (1) the extension of a pathological change is rated with a ‘score value’; and (2) the pathological importance of this alteration is defined as an ‘importance factor’. The sum of the multiplied score values and importance factors of all diagnosed changes results in different indices. With these indices, statistical analysis can be carried out. Assessment methods for the gills, liver, kidney and skin are described.