Short-term side effects: Ketosis, which can result in bad breath, tiredness, weakness, dizziness, insomnia, and nausea may occur. Constipation may also occur as a consequence of avoiding high-fiber foods such as fruit, vegetable, and beans.

Long-term side effects: Some medical experts question the health safety of the Atkins diet over the long term because the Atkins diet allows consumption of foods containing saturated fats and proteins without any restriction. Health concerns include the impact of large amounts of protein on kidney function, the impact of saturated fats on cholesterol and heart disease, and the potential for some types of cancers to develop from eating a diet low in complex carbohydrates, antioxidants, certain vitamins and minerals, and fiber.

Individuals considering the Atkins diet should consult their physician, and follow the diet phases as recommended in the book.

Under the Atkins diet outline, dieters are recommended to stop any unnecessary medications. Any changes to medication should be discussed with a qualified healthcare professional. Diuretics, and, to a lesser extent, other cardiovascular medications and diabetes medications, including insulin, when combined with this diet may produce dangerous effects. Psychotropic drugs, phenothiazines and anti-depressants such as Prozac®, tranquilizers, lithium, and similar drugs may cause metabolic resistance to the diet. Estrogen, prednisone and other steroids, and antiarthritic drugs, especially NSAIDS, can cause weight gain or prevent weight loss. For persons metabolically resistant, any medications may aggravate the condition.

This diet is not recommended for pregnant or lactating women, especially if women are on the induction phase because carbohydrate intake is very restricted. Individuals with high blood pressure and a history of heart attack should not go on the Atkins diet.

Women at risk for osteoporosis should exercise extreme caution when considering the Atkins diet. The acidity caused by this high protein diet may result in an increased likelihood of loss in bone mass.

Individuals with nutritional absorption problems should consult their physician before beginning the Atkins diet.

Vegetarians and others with pre-existing dietary restrictions may require extra vigilant attention to nutritional intake in order to remain healthy on the diet.

Individuals who choose the Atkins diet should pay careful attention to their nutritional intake. Following the Atkins diet does not change or eliminate the body's need for adequate amounts of vitamins and minerals.

There are no long-term studies establishing the safety or effectiveness of the Atkins diet.

Atkins proposed that the significant increase in insulin-producing foods, especially refined carbohydrates, were the primary cause of increases in American metabolic disorders, including obesity. The consumption of carbohydrates results in the secretion of insulin. Atkins theorized that most Americans suffer from what he termed "hyperinsulinism," a chronic state of high levels of insulin in the body.

The human body derives energy from food via three pathways. Usually, the body burns glucose from carbohydrates as the source of energy. During the introduction period of the Atkins diet, the body is forced to burn fat as the primary source of energy. The body quickly enters a phase known as ketosis as a result. Ketosis requires more steps, and thus, offers less energy than the energy pathway of carbohydrate metabolism. Further steps include a small amount of carbohydrates into the diet. These carbohydrates are important because the brain can only derive energy from glucose. For this reason, avoidance of carbohydrates after the introduction phase may result in ketoacidosis, a serious condition resulting from the absence of glucose for prolonged periods of time.

The diet is based on the theory that overweight people eat too many carbohydrates. Bodies burn both fat and carbohydrates for energy, but carbohydrates are used first. By drastically reducing carbohydrate intake and increasing protein and fat intake, the body will, in theory, naturally lose weight by burning stored body fat more efficiently.

An article in the journal Obesity Research (2001) found that the drastic weight loss, which occurs at the start of the Atkins diet does not continue after about six months. The study found that individuals on the Atkins diet experienced long-term weight loss results similar to individuals on weight loss plans with similar regimens of calories.

A study in the Journal of the American Medical Association found that most individuals on the Atkins diet did not comply with the eating for the year length of the study duration. In addition, those who initially lost weight or did not abide by the Atkins diet did not sustain their weight loss or lowered risk of diabetes.

Some experts have attributed the success of the Atkins diet to a significantly reduced intake of calories, rather than changes in the body's metabolism. However, the way that the Atkins diet changes the body's metabolism is unknown.