Digestive diseases are the main cause of morbidity and mortality in growing rabbits. Clostridium perfringens is a widely occurring pathogenic bacterium in enteric diseases of domestic animals and its pathogenicity stems from the production of potent exotoxins. This work aimed to quantify the concentration of C. perfringens α-toxin in caecal samples of rabbits with digestive diseases and relate these concentrations to C. perfringens counts. Additionally, C. perfringens strains isolated from rabbits with clinical lesions of Epizootic Rabbit Enteropathy (ERE) were toxinotyped. To conduct this work, a total of 711 rabbits weaned at 35 d were housed in pairs and fattened until the age of 63 d. No experimental infection was performed and no antibiotics were provided in the feed or drinking water. All rabbits displaying symptoms of digestive diseases were slaughtered and necropsied. At 46 d, 88 healthy rabbits were also slaughtered. Caecal contents were sampled from all slaughtered animals. Thirty-seven out of the 69 rabbits with digestive diseases (88.5% of sick animals) showed ERE-confirmed symptoms and lesions. Apart from diarrhoea, the most constant ERE signs were abdominal bloating and borborygmi. At necropsy, the anterior digestive tract was found filled with large amounts of gas and liquid. Twenty-seven rabbits had liquid caecal contents whereas caecal impaction only appeared in 10 rabbits. Live weight was lower by 49.2% (P<0.001) in diseased rabbits as compared with healthy rabbits of the same age. For C. perfringens counts lower than 6.0 log cfu/g, the α-toxin concentration remained below 2.6 μg/mg. However, for bacterial counts above 6.0 log cfu/g the concentration of α-toxin ranged from 0.12 to 60.9 μg/mg. Nevertheless, both caecal concentration of C. perfringens (7.65 vs. 3.09 log cfu/g, P<0.001) and that of its α-toxin (6.02 vs. 0.17 μg/mg, P<0.001) were higher in diseased rabbits than in healthy ones. C. perfringens toxinotype A was found in all ERE-affected rabbits. No other toxinotype was identified and no isolate contained the enterotoxin gene. In conclusion, C. perfringens α-toxin should not be considered a good indicator of the bacterium's presence, as high counts of colonies are not always associated with high toxin concentrations.