Spirulina is a form of cyanobacterium, some of which are known to produce toxins such as microcystins, BMAA, and others. Some spirulina supplements have been found to be contaminated with microcystins, albeit at levels below the limit set by the Oregon Health Department. Microcystins can cause gastrointestinal disturbances, and in the long term, liver damage. The effects of chronic exposure to even very low levels of microcystins are of concern, because of the potential risk of toxicity to several organ systems and possibly cancer.
These toxic compounds are not produced by spirulina itself, but may occur as a result of contamination of spirulina batches with other toxin-producing blue-green algae. Because spirulina is considered a dietary supplement in the U.S., no active, industry-wide regulation of its production occurs and no enforced safety standards exist for its production or purity. The U.S. National Institutes of Health describes spirulina supplements as "possibly safe", provided they are free of microcystin contamination, but "likely unsafe" (especially for children) if contaminated. Given the lack of regulatory standards in the U.S., some public-health researchers have raised the concern that consumers cannot be certain that spirulina and other blue-green algae supplements are free of contamination.
Heavy-metal contamination of spirulina supplements has also raised concern. The Chinese State Food and Drug Administration reported that lead, mercury, and arsenic contamination was widespread in spirulina supplements marketed in China. One study reported the presence of lead up to 5.1 ppm in a sample from a commercial supplement.