Most β pore-forming toxins need to be oligomerized via receptors in order to form membrane pores. Though oligomerizing toxins frequently form SDS-resistant oligomers, it was questionable whether SDS-resistant oligomers reflected native functional toxin complexes. In order to elucidate the essence of the cytocidal assemblages, oligomers of aerolysin-like toxins, aerolysin, parasporin-2 and epsilon toxin, were examined with or without SDS. On Blue Native PAGE, each toxin, which had been solubilized from target cells with mild detergent, was a much larger complex (nearly 1 MDa) than the typical SDS-resistant oligomers (∼200 kDa). Size exclusion chromatography confirmed the huge toxin complexes. While a portion of the huge complexes were sensitive to proteases, SDS-resistant oligomers resist the proteolysis. Presumably the core toxin complexes remained intact while the cellular proteins were degraded. Moreover, intermediate complexes, which included no SDS-resistant oligomers, could be detected at lower temperatures. This study provides evidence for huge functional complexes of β pore-forming toxins and emphasizes their potential variance in composition.