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.

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:

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.

The term alimentary mycotoxicoses refers to the effect of poisoning by Mycotoxins (The term 'mycotoxin' is usually reserved for the toxic chemical products produced by fungi that readily colonize crops) through food consumption. Mycotoxins sometimes have important effects on human and animal health. For example, an outbreak which occurred in the UK in 1960 caused the death of 100,000 turkeys which had consumed aflatoxin-contaminated peanut meal. In the USSR in World War II, 5,000 people died due to Alimentary Toxic Aleukia (ALA). The common foodborne Mycotoxins include:

- Aflatoxins – originated from Aspergillus parasiticus and Aspergillus flavus. They are frequently found in tree nuts, peanuts, maize, sorghum and other oilseeds, including corn and cottonseeds. The pronounced forms of Aflatoxins are those of B1, B2, G1, and G2, amongst which Aflatoxin B1 predominantly targets the liver, which will result in necrosis, cirrhosis, and carcinoma. In the US, the acceptable level of total aflatoxins in foods is less than 20 μg/kg, except for Aflatoxin M1 in milk, which should be less than 0.5 μg/kg. The official document can be found at FDA's website.

- Altertoxins – are those of Alternariol (AOH), Alternariol methyl ether (AME), Altenuene (ALT), Altertoxin-1 (ATX-1), Tenuazonic acid (TeA) and Radicinin (RAD), originated from Alternaria spp. Some of the toxins can be present in sorghum, ragi, wheat and tomatoes. Some research has shown that the toxins can be easily cross-contaminated between grain commodities, suggesting that manufacturing and storage of grain commodities is a critical practice.

- Citrinin

- Citreoviridin

- Cyclopiazonic acid

- Cytochalasins

- Ergot alkaloids / Ergopeptine alkaloids – Ergotamine

- Fumonisins – Crop corn can be easily contaminated by the fungi Fusarium moniliforme, and its Fumonisin B1 will cause Leukoencephalomalacia (LEM) in horses, Pulmonary edema syndrome (PES) in pigs, liver cancer in rats and Esophageal cancer in humans. For human and animal health, both the FDA and the EC have regulated the content levels of toxins in food and animal feed.

- Fusaric acid

- Fusarochromanone

- Kojic acid

- Lolitrem alkaloids

- Moniliformin

- 3-Nitropropionic acid

- Nivalenol

- Ochratoxins – In Australia, The Limit of Reporting (LOR) level for Ochratoxin A (OTA) analyses in 20th Australian Total Diet Survey was 1 µg/kg, whereas the EC restricts the content of OTA to 5 µg/kg in cereal commodities, 3 µg/kg in processed products and 10 µg/kg in dried vine fruits.

- Oosporeine

- Patulin – Currently, this toxin has been advisably regulated on fruit products. The EC and the FDA have limited it to under 50 µg/kg for fruit juice and fruit nectar, while limits of 25 µg/kg for solid-contained fruit products and 10 µg/kg for baby foods were specified by the EC.

- Phomopsins

- Sporidesmin A

- Sterigmatocystin

- Tremorgenic mycotoxins – Five of them have been reported to be associated with molds found in fermented meats. These are Fumitremorgen B, Paxilline, Penitrem A, Verrucosidin, and Verruculogen.

- Trichothecenes – sourced from Cephalosporium, Fusarium, Myrothecium, Stachybotrys and Trichoderma. The toxins are usually found in molded maize, wheat, corn, peanuts and rice, or animal feed of hay and straw. Four trichothecenes, T-2 toxin, HT-2 toxin, diacetoxyscirpenol (DAS) and deoxynivalenol (DON) have been most commonly encountered by humans and animals. The consequences of oral intake of, or dermal exposure to, the toxins will result in Alimentary toxic aleukia, neutropenia, aplastic anemia, thrombocytopenia and/or skin irritation. In 1993, the FDA issued a document for the content limits of DON in food and animal feed at an advisory level. In 2003, US published a patent that is very promising for farmers to produce a trichothecene-resistant crop.

- Zearalenone

- Zearalenols

Prevention is mainly the role of the state, through the definition of strict rules of hygiene and a public services of veterinary surveying of animal products in the food chain, from farming to the transformation industry and delivery (shops and restaurants). This regulation includes:

- traceability: in a final product, it must be possible to know the origin of the ingredients (originating farm, identification of the harvesting or of the animal) and where and when it was processed; the origin of the illness can thus be tracked and solved (and possibly penalized), and the final products can be removed from the sale if a problem is detected;

- enforcement of hygiene procedures such as HACCP and the "cold chain";

- power of control and of law enforcement of veterinarians.

In August 2006, the United States Food and Drug Administration approved Phage therapy which involves spraying meat with viruses that infect bacteria, and thus preventing infection. This has raised concerns, because without mandatory labelling consumers would not be aware that meat and poultry products have been treated with the spray.

At home, prevention mainly consists of good food safety practices. Many forms of bacterial poisoning can be prevented by cooking it sufficiently, and either eating it quickly or refrigerating it effectively. Many toxins, however, are not destroyed by heat treatment.

Techniques that help prevent food borne illness in the kitchen are hand washing, rinsing produce, preventing cross-contamination, proper storage, and maintaining cooking temperatures. In general, freezing or refrigerating prevents virtually all bacteria from growing, and heating food sufficiently kills parasites, viruses, and most bacteria. Bacteria grow most rapidly at the range of temperatures between , called the "danger zone". Storing food below or above the "danger zone" can effectively limit the production of toxins. For storing leftovers, the food must be put in shallow containers

for quick cooling and must be refrigerated within two hours. When food is reheated, it must reach an internal temperature of or until hot or steaming to kill bacteria.