The top two offenders:
1. Gluten. Individuals with digestive problems are likely to have heard of Celiac Disease, a disease in which the intestinal lining, called villi, is damaged by gluten (a protein found in wheat, rye, oats, kamut and spelt), and nutrients are not absorbed properly. Approximately 1:100 people have Celiac Disease, and of those, most are either improperly diagnosed or completely undiagnosed. Celiac Disease and the related condition of Gluten Intolerance can present like Chronic Fatigue Syndrome, Depression, and Fibromyalgia, as well as Irritable Bowel Syndrome. Removing gluten from the diet can help the quality of life of many people with conditions that are confounding their doctors, not only those with digestive ailments. After eliminating all gluten from the diet, most people will see a marked change within 72 hours, though it can take a couple weeks for some to see the effects.
2. Dairy. Humans are the only species on the planet who drink the milk of another species, and the only mammals that drink milk of any type after weaning. Some cultures have a high rate of lactose intolerance, and dairy is not a big part of the diet in those areas. Milk and other dairy products can cause a build-up of mucous, leading to sinus problems and ear infections. Some studies have linked a diverse list of ailments to milk consumption - diabetes, Crohn's Disease, osteoporosis, and rheumatoid arthritis, and further studies have found that hormones such as rBGH are linked to early puberty in preteen girls. Dairy can take 2 weeks to a couple months to remove from the system, so patience is needed if you are eliminating dairy.
Many health conditions have a link to diet, and keeping a food log can help you determine if your symptoms follow a pattern. For example, do you always get a headache after ordering Chinese food? MSG could be an issue for you. Does your rheumatoid arthritis flare after eating Italian food? For some people foods in the nightshade family (tomato, eggplant, peppers, and potatoes) can lead to a flare. Other food ingredients such as sulfites and phenols have been linked to health concerns, and additives such as red dye #4 and nitrates can cause issues as diverse as headaches and hyperactivity.
If you have developed health problems that are difficult to diagnose, and troublesome to treat, and a food log hasn't been helpful, another option is an elimination or rotation diet. If the food that is causing you trouble is in your day-to-day diet, then the food log wouldn't have been helpful, so you need to eliminate it. Elimination diets work by you narrowing your diet to a few foods that are the least likely to be allergenic (often lamb, rice, and pears are chosen). If after two weeks the symptoms persist, then a new group of foods is chosen. If the symptoms are gone, then new foods are added in one at a time, and with several days between each new food until troublesome foods are identified. A rotation diet works by only serving a food once every 4-5 days, and works with a food log to discover the link between a symptom and a food.