The gross pathology and the histopathological alterations identified in juvenile specimens of the European hake (Merluccius merluccius), one of the most important target species of commercial fisheries in the northwest Mediterranean, are described. A qualitative and semi‐quantitative histological approach was performed in specimens from 2007 and 2019. Prevalence and mean intensity of parasites and histopathological changes were calculated in both years. No macroscopic alterations were found in any organ but several parasites (e.g., copepods, nematodes, digeneans) were detected. Microscopically, alterations identified in gills included foci of inflammation and hyperplasia (present in 77.38% of hakes from both years), extensive hyperplasia (33.33%), and inflammation (16.65%) that were potentially related to the mechanical effects of monogeneans and copepods, cysts of unknown etiology (62.69%), and lamellar inflammation associated to Aporocotyle spinosicanalis eggs (8.33%). Granulomas and inflammatory focus were detected in the liver, spleen, and stomach, apparently associated with the presence of nematodes. Coelozoic myxosporean parasites were detected within the renal tubules (66.66%). Most of the pathologies detected were similar to those described in other gadoid species (i.e., Gadus morhua) and were usually related to the presence of ecto and endoparasites. The potential impact of parasites on the health of this fish species is discussed for improving the knowledge and management of these valuable fishing stocks.