Whole wheat flour is a coarse, brown flour with a sweet, nutty flavor made from the entire wheat kernel (hence the name "whole wheat"). A wheat kernel is made up of three main components, the endosperm, bran, and germ. Since whole wheat flour contains all of these components it retains the nutrients contained within them. The bran contains most of the fiber and minerals, including vitamin B and E, present in the kernel. The endosperm accounts for most of the flour's weight and contains most of the kernel's protein and carbohydrates. Finally, the germ contains a decent amount of healthy polyunsaturated fat.

There are two common ways to produce whole wheat flour. The older technique is called "stone-ground" where the wheat kernels are ground between large stones. These stones are often placed in water mills and are moved by the flow of water from a river. When the flour is stone-ground the bran, endosperm, and germ are all crushed together. The oil present in the germ is often released into the flour. This makes stone-ground wheat more susceptible to spoilage. The other technique, developed during the Industrial Revolution, is called "roller-milled." This method is used by large-scale flour producers and is also used to produce white flour. Here the kernels are crushed between high-speed rollers which separate the bran and germ from the endosperm. When making whole wheat flour this way the bran and germ must be added back after processing. This form of milling often subjects the flour to high heat, which is thought to destroy some nutrients, vitamins, and enzymes in the flour. However, this heat also increases the life span of the flour by decreasing spoilage. Since roller-milled flour is mass-produced it is generally cheaper than stone-ground flour.

Whole wheat flour is much more nutritious than white flour. White flour has been milled so that most of the germ and bran have been removed, leaving only the endosperm. This process removes about 80 percent of the nutrients that are present in whole wheat flour. White flour has only trace amounts of fiber, vitamin B, and vitamin E. This flour was originally so nutritionally empty that in 1943 the United States government mandated that white flour must be enriched with thiamin, riboflavin and niacin. In 1998 the government also stated that folate must also be added to white flour. White flour with these additions is labeled as "enriched." However, even after all these additions this enriched white flour is nowhere near as nutritious as whole wheat flour. Many nutrients that are lost during production, such as fiber, vitamin E, magnesium, protein, zinc and copper, are never added back to the flour. White flour is also often subjected to potentially unhealthy chemicals that whiten and mature the flour.

Because of its additional nutrients, whole wheat flour has more health benefits than white flour. The fiber present in the flour helps to keep the gastrointestinal tract functioning normally and may help prevent more serious problems such as colon cancer, diverticulosis, and hemorrhoids. Whole wheat flour may also reduce the risk for diabetes and coronary artery disease. It also contains healthy phytochemicals, including antioxidants, which may help ward off cancer.

When purchasing goods made from whole wheat flour it is important to examine the packaging. Look for products that have "100% whole wheat" on the label. Labels such as "stone-ground," "seven-grain," and "multigrain" often do not contain whole wheat flour and are not as nutritious. Don't be misled by darker colored breads either, as some companies simply add caramel coloring or molasses to give a browner color. The best way to make sure a product has whole wheat flour is to examine the ingredient listing. Look for "whole wheat flour" as the first ingredient. Avoid products whose first ingredient is "wheat flour" or "enriched flour," as they generally do not contain whole wheat flour.

Whole wheat flour behaves differently than white flour when used in baked goods. The bran present in whole wheat flour reduces the development of gluten and hinders rising. This makes baked goods produced from whole wheat flour denser and heavier than those made with white flour. Whole wheat pastry flour can be used to make lighter baked goods. It is made from soft wheat instead of hard wheat and therefore has a lower level of protein than regular whole wheat flour. This makes it suitable for more delicate baked goods. Whole wheat flour can be substituted for white flour in most recipes, however this substitution will lead to a denser product. Many bakers use a combination of whole wheat and white flour to gain the nutritional benefits of whole wheat without losing too much rise. The exact combination varies, but you can generally substitute half the white flour for whole wheat without really affecting the density of the product.

Whole wheat flour is more susceptible to spoilage than other flours because it contains the oils from the bran that can become rancid. If the flour is stored at room temperature, try to use it within a week or two. Otherwise you can store the flour in the fridge or freezer for longer periods of time of up to a year.

"Artisan Baking across America", Maggie Glezer, 2000