Children, pregnant women, and women who may become pregnant should not consume a raw foods diet due to the risk of very severe developmental defects, such as mental retardation and slow growth.

Uncooked foods may contain bacteria and parasites, which are usually destroyed by the heating of foods.

Individuals with pre-existing dietary restrictions should consult a qualified healthcare practitioner before adopting the raw foods diet.

Individuals who consume a diet that does not include different types of foods are at risk of developing food allergies, which usually develop over a period of month or years. Usually, a person has to limit their intake of or avoid these foods in order to prevent side effects, which may range from a skin rash to a deadly all-over bodily inflammation known as anaphylactic shock.

Raw foods advocates claim that animals suffer fewer degenerative diseases, such as Alzheimer's disease and cancer, because they do not consume toxins produced by the cooking of food, a practice limited to humans. However, some individuals think that if animals significantly increased their lifespan by taking medicines for example, as humans have done, they would eventually develop degenerative diseases due to the cumulative wear and tear on bodily systems.

Advocates believe that foods in their uncooked state have a higher nutrient value. In addition, raw foods advocates claim that enzymes in sprouted and raw foods are more abundant than in a cooked form, and that these enzymes aid in digestion. As a result, the body can supposedly devote more energy to other bodily processes because it did not have to expend as much energy for digestion. However, enzymes destroyed by the cooking of food may be destroyed in the human digestive tract, due to the very low pH of the stomach, which usually destroys enzymatic functioning. Some raw foodists believe that these enzymes may become active again in the small intestine, but this may be unlikely, as inactive enzymes irreversibly assume a new shape, which may permanently change their function.

Because adherents of the raw foods diet comprise a relatively small population, the diet has not been extensively studied. Further, the lack of adverse effects associated with eating properly prepared foods has not motivated researchers to investigate the raw foods diet as a modality to prevent any condition or disease.

The inclusion of fewer processed foods (such as pre-packaged muffins) in the diet is advocated by the U.S. Food and Drug Administration (FDA) in the revised 2005 food pyramid. To this extent, most nutritionists believe that the benefits of the raw foods diet lie in the avoidance of processed foods, rather than on the avoidance of cooked foods.

A 1999 survey by Koebnick et al. evaluated the relationship between a strict raw foods diet and amenorrhea, low body weight, and body weight loss in 513 adults whose diets consisted primarily of raw foods. The study authors gave the raw foodists surveys to inquire about a variety of health problems. Due to the frequency of health effects reported by survey respondents, including amenorrhea, low body weight, and body weight loss, the authors concluded that a long-term raw foods diet was not recommended.