C. thermocellum can utilize lignocellulosic waste and generate ethanol, thus making it a possible candidate for use in production of ethanol fuel. It also has no oxygen requirement and is thermophilic, which reduces cooling cost.

C. acetobutylicum, also known as the Weizmann organism, was first used by Chaim Weizmann to produce acetone and biobutanol from starch in 1916 for the production of gunpowder and TNT.

C. botulinum, which produces a fatal neurotoxin, is commonly injected in a diluted form in the drug Botox, which is carefully injected to nerves in the face, which prevents the movement of the expressive mucles of the forehead, to delay the wrinkling effect of aging.

The anaerobic bacterium C. ljungdahlii, recently discovered in commercial chicken wastes, can produce ethanol from single-carbon sources including synthesis gas, a mixture of carbon monoxide and hydrogen that can be generated from the partial combustion of either fossil fuels or biomass. Use of these bacteria to produce ethanol from synthesis gas has progressed to the pilot plant stage at the BRI Energy facility in Fayetteville, Arkansas.

Fatty acids are converted by yeasts to long-chain dicarboxylic acids and then to 1,3-propanediol using Clostridium diolis.

Genes from C. thermocellum have been inserted into transgenic mice to allow the production of endoglucanase. The experiment was intended to learn more about how the digestive capacity of monogastric animals could be improved. Hall et al. published their findings in 1993.

Non-pathogenic strains of Clostridia may help in the treatment of diseases such as cancer. Research shows that Clostridia can selectively target cancer cells. Some strains can enter and replicate within solid tumours. Clostridia could, therefore, be used to deliver therapeutic proteins to tumours. This use of Clostridia has been demonstrated in a variety of preclinical models.