The intercalibration exercise is an important step in the building process of the surface water ecological quality assessment, which is required by the Water Framework Directive (WFD). Its aim is to apply the water quality classification in a uniform manner to all the Member States belonging to the same eco-region. Cyprus, France, Greece, Italy, Slovenia and Spain participated in the soft-bottom benthic invertebrate subgroup for the Mediterranean coastal region. The methodologies proposed by Member States were applied and tested; the results were compared and harmonized to establish agreed and comparable boundaries for the benthic invertebrate ecological status classes. The national methods used in the intercalibration process were: for Cyprus and Greece, the Bentix Index; for Slovenia, a combination of AZTI Marine Biotic Index (AMBI), richness and diversity with the use of factor and discriminant analysis (Multimetric AMBI); for Spain, a new index, named MEDOCC, which is an adaptation of the AMBI index to the Western Mediterranean area. Italy and France tested different methods, none of which have been officially adopted. Final class boundary values for the different official classification systems were obtained and compared. Besides describing methods and results obtained by the different countries, the Italian situation is examined in more detail. All the above methods have been applied to Italian data, but the results were not conclusive. Major causes for concern are related to insufficient sites and data, to the lack of real non-impacted reference sites, and to the difficulties in validating the ecological status classification in sites not showing a pollution gradient.