Bovine spongiform encephalopathy (BSE) in cattle, the most likely cause of variant Creutzfeldt–Jakob disease in humans, is thought to be caused by a unique infectious agent, with stable features, even when transmitted to other species. Here, we show the existence of an atypical molecular phenotype among cattle diagnosed with BSE in France. Following western blot analysis, three cases showed unusual features of the electrophoretic profiles of the protease‐resistant prion protein (PrP^res) accumulating in the brain. The PrP^res patterns were similar in these three atypical cases, showing a higher molecular mass of unglycosylated PrP^res and strong labelling by P4 monoclonal antibody compared to 55 typical BSE cases. This finding suggests either some phenotypic modifications of PrP^res following infection by the BSE agent or the existence of alternative origins of such diseases in cattle.