A raw food, sashimi can cause foodborne illness because of bacteria and parasites, for example anisakiasis; a human disease caused by the accidental ingestion of larval nematodes in the family Anisakidae, primarily Anisakis simplex but also Pseudoterranova decipiens.[3] In addition, incorrectly prepared Fugu fish may contain tetrodotoxin, a potent neurotoxin with no known antidote.

Traditionally, fish that spend at least part of their lives in brackish or fresh water were considered unsuitable for sashimi because of the possibility of parasites. For example, salmon, an anadromous fish, is not traditionally eaten straight out of the river. A study in Seattle, Washington, showed that all wild salmon had roundworm larvae capable of infecting people, while farm-raised salmon did not have any roundworm larvae.[4]

Freezing is often used to kill parasites. According to European Union regulations,[5] freezing fish at −20°C (−4°F) for 24 hours kills parasites. The U.S. Food and Drug Administration (FDA) recommends freezing at −35°C (−31°F) for 15 hours, or at −20°C (−4°F) for 7 days.[6]

While Canada does not federally regulate freezing fish[citation needed], British Columbia[7] and Alberta[8] voluntarily adhere to guidelines similar to the FDA's.[citation needed] Ontario attempted to legislate freezing as part of raw food handling requirements, though this was soon withdrawn due to protests by the industry that the subtle flavors and texture of raw fish would be destroyed by freezing. Instead, Ontario has decided to consider regulations on how raw fish must be handled prior to serving.[9]

Some fish for sashimi are treated with carbon monoxide to keep the flesh red for a longer time in storage. This practice can make spoiled fish appear fresh.[10][11]

Intake of large amount of certain kind of fish may affect health due to mercury content.