Late-blowing – severe cheese spoilage caused by clostridia – is a long-standing problem of economic importance for dairy processors. However, there is still a paucity of relevant data on clostridia in cheese that would allow some tailored intervention. The main aim of this study was to identify and quantify clostridia in late-blown cheese using a polyphasic methodological approach. Fifty-three cheeses of different origins were analysed using culture-dependent (MPN, enrichment, molecular identification of isolates) and culture-independent methods (real-time PCR, PCR-DGGE and Illumina 16S rDNA sequencing). Using culture-dependent methods, clostridial isolates were collected from several cheese samples, while fewer positive results were obtained with the samples when using the MPN procedure than real-time PCR or PCR-DGGE. In contrast to other studies, an extremely low diversity of Clostridium species was observed. Surprisingly, Illumina 16S rDNA amplicon sequencing revealed relative abundances of clostridia below the detection limit despite apparent cheese spoilage.