In the last decade, a new parasite that causes severe losses has been detected in farmed turbot Psetta maxima (L.), in north-western Spain. The parasite was classified as a myxosporean and named Enteromyxum scophthalmi. The aim of this study was to characterize the main histological changes that occur in E. scophthalmi-infected turbot. The parasite provoked catarrhal enteritis, and the intensity of the lesions was correlated with the progression of the infection and with the development of the parasite. Infected fish were classified into 3 groups, according to the lesional degree they showed (slight, moderate and severe infections). In fish with slight infections, early parasitic stages were observed populating the epithelial lining of the digestive tract, without eliciting an evident host response. As the disease progressed, catarrhal enteritis was observed, the digestive epithelium showed a typical scalloped shape and the number of both goblet and rodlet cells was increased. Fish with severe infections suffered desquamation of the epithelium, with the subsequent release of parasitic forms to the lumen. The dislodged enterocytes underwent anoikis, a mode of apoptosis triggered by the loss of anchorage, which might facilitate spreading of the parasite. Lymphohaematopoietic depletion was also observed, mainly in head kidney and spleen, which could contribute to the high virulence of this parasite.