The aim of the present work was to determine if a practical plant protein-based diet containing vegetable oils (VO) as the major lipid source could alter the disease course when challenged with the myxosporean Enteromyxum leei, a wide-spread parasite in the Mediterranean basin causing heavy economic losses. Gilthead sea bream (Sparus aurata) fed for 9 months either a fish oil (FO) diet or a blend of VOs at 66% of replacement (66VO diet) were challenged by exposure to parasite-contaminated water effluent. All fish were periodically and non-lethally sampled to obtain biometrical data and to know their infection status. After 102 days of exposure, fish were euthanized and haematological, biometrical, histological, immunological, glutathione and anti-oxidant data were obtained from tissue, blood and serum samples. Anorexia appeared in both exposed groups, but feed intake reduction was higher in 66VO fish. The signs of disease (lower growth, condition factor, specific growth rate, haematocrit) as well as the disease course were worse in fish from 66VO group, with a higher prevalence and intensity of infection, a higher percentage of fish harbouring the parasite in the entire intestinal tract, and a faster establishment of the parasite. Parasite intensity of infection was negatively correlated with growth parameters and haematocrit in both groups, and with complement, lysozyme and hepatic total glutathione in 66VO fish.