For the worm, humans are a dead-end host. "Anisakis" and "Pseudoterranova" larvae cannot survive in humans, and eventually die. In some cases, the infection resolves with only symptomatic treatment. In other cases, however, infection can lead to small bowel obstruction, which may require surgery, although treatment with albendazole alone (avoiding surgery) has been reported to be successful. Intestinal perforation (an emergency) is also possible.

Even when the fish is thoroughly cooked, "Anisakis" larvae pose a health risk to humans. Anisakids (and related species such as the sealworm, "Pseudoterranova" species, and the codworm "Hysterothylacium aduncum") release a number of biochemicals into the surrounding tissues when they infect a fish. They are also often consumed whole, accidentally, inside a fillet of fish.

Acute allergic manifestations, such as urticaria and anaphylaxis, may occur with or without accompanying gastrointestinal symptoms. The frequency of allergic symptoms in connection with fish ingestion has led to the concept of gastroallergic anisakiasis, an acute IgE-mediated generalized reaction. Occupational allergy, including asthma, conjunctivitis, and contact dermatitis, has been observed in fish processing workers.

Sensitivization and allergy are determined by skin-prick test and detection of specific antibodies against "Anisakis". Hypersensitivity is indicated by a rapid rise in levels of IgE in the first several days following consumption of infected fish.

The capture, transportation and culture of bait fish can spread damaging organisms between ecosystems, endangering them. In 2007, several American states, including Michigan, enacted regulations designed to slow the spread of fish diseases, including viral hemorrhagic septicemia, by bait fish. Because of the risk of transmitting "Myxobolus cerebralis" (whirling disease), trout and salmon should not be used as bait. Anglers may increase the possibility of contamination by emptying bait buckets into fishing venues and collecting or using bait improperly. The transportation of fish from one location to another can break the law and cause the introduction of fish and parasites alien to the ecosystem.

Though not a health concern in thoroughly cooked fish, parasites are a concern when human consumers eat raw or lightly preserved fish such as sashimi, sushi, ceviche, and gravlax. The popularity of such raw fish dishes makes it important for consumers to be aware of this risk. Raw fish should be frozen to an internal temperature of −20 °C (−4 °F) for at least 7 days to kill parasites. It is important to be aware that home freezers may not be cold enough to kill parasites.

Traditionally, fish that live all or part of their lives in fresh water were considered unsuitable for sashimi due to the possibility of parasites (see Sashimi article). Parasitic infections from freshwater fish are a serious problem in some parts of the world, particularly Southeast Asia. Fish that spend part of their life cycle in salt water, like salmon, can also be a problem. A study in Seattle, Washington showed that 100% of wild salmon had roundworm larvae capable of infecting people. In the same study farm raised salmon did not have any roundworm larvae.

Parasite infection by raw fish is rare in the developed world (fewer than 40 cases per year in the U.S.), and involves mainly three kinds of parasites: Clonorchis sinensis (a trematode/fluke), Anisakis (a nematode/roundworm) and Diphyllobothrium (a cestode/tapeworm). Infection by the fish tapeworm "Diphyllobothrium latum" is seen in countries where people eat raw or undercooked fish, such as some countries in Asia, Eastern Europe, Scandinavia, Africa, and North and South America. Infection risk of anisakis is particularly higher in fishes which may live in a river such as salmon ("shake") in Salmonidae, mackerel ("saba"). Such parasite infections can generally be avoided by boiling, burning, preserving in salt or vinegar, or freezing overnight. Even Japanese people never eat raw salmon or ikura (salmon roe), and even if they seem raw, these foods are not raw but are frozen overnight to prevent infections from parasites, particularly anisakis.

Below are some life cycles of fish parasites that can infect humans:

Globally, infants are a population that are especially vulnerable to foodborne disease. The World Health Organization has issued recommendations for the preparation, use and storage of prepared formulas. Breastfeeding remains the best preventative measure for protection of foodborne infections in infants.

Food may be contaminated during all stages of food production and retailing. In order to prevent viral contamination, regulatory authorities in Europe have enacted several measures:

- European Commission Regulation (EC) No 2073/2005 of November 15, 2005

- European Committee for Standardization (CEN): Standard method for the detection of norovirus and hepatitis A virus in food products (shellfish, fruits and vegetables, surfaces and bottled water)

- CODEX Committee on Food Hygiene (CCFH): Guideline for the application of general principles of food hygiene for the control of viruses in food