Unlike refined white flour, all of the grain is used to make whole wheat flour.

General information:

From Wikipedia: “Whole-wheat flour (in the US) or wholemeal flour (in the UK) is a powdery substance, a basic food ingredient, derived by grinding or mashing the whole grain of wheat, also known as the wheatberry. Whole-wheat flour is used in baking of breads and other baked goods, and also typically mixed with other lighter "white" unbleached or bleached flours (that have been treated with flour bleaching agent(s)) to restore nutrients to the white flours (especially fiber, protein, and vitamins), texture, and body that are lost in milling and other processing to the finished baked goods or other food(s).”

Benefits (compared to white flour):

“The word "whole" refers to the fact that all of the grain (bran, germ, and endosperm) is used and nothing is lost in the process of making the flour. This is in contrast to white, refined flours, which contain only the endosperm. Because the whole flour contains the remains of all of the grain, it has a textured, brownish appearance.”

“Whole-grain whole wheat flour is a full-flavored flour containing vitamins, minerals and protein. Whole-grain whole wheat flour is more nutritious than refined white flour, although white flour may, in a process called food fortification, have some micronutrients lost in processing added back to the white flour (required by law in some jurisdictions). Fortified white flour does not, however, contain the macronutrients of the wheat's bran and germ (especially fiber and protein) like whole-grain flour does, and is notably lacking in fiber. Whole grain is a good source of calcium, iron, fiber, and other minerals like selenium.”

Drawbacks (compared to white flour):

“Whole-wheat flour has a shorter shelf life than white flour, as the higher oil content leads to rancidification if not stored properly, such as with refrigeration, or in other cool areas.

Often, whole wheat flour is not the main ingredient in baked goods, as it may add a certain "heaviness" that prevents them from rising as high as white flours. This can add to the cost per volume of the baked item, as it requires more flour to obtain the same volume, due to the fewer and smaller air pockets trapped in the raised goods. Thus, many baked goods advertised as whole-wheat are not entirely whole-wheat; they may contain some refined white wheat, as long as the majority of the wheat used is whole-wheat.

Nevertheless, it is possible to make a high-rising, light loaf of 100% whole-wheat bread, as long as one increases the water content of the dough (the bran and germ in whole wheat absorb more water than plain white flour), kneads the dough for a longer period of time to develop the gluten adequately, and allows for a longer rise before shaping the dough. Some bakers let the dough rise twice before shaping. The addition of fats, such as butter or oil, and milk products (fresh milk, powdered milk, buttermilk, yogurt, etc.) can also greatly assist the dough in rising.”

Terminology and regulations in North America and the rest of the world:

• “In the United States, "whole wheat flour" must contain the whole grain—the bran, the germ, and the endosperm—in the naturally occurring proportions.
  
• In Canada, when wheat is milled, parts of the kernel are separated and then recombined to make whole wheat flour. The standard for whole wheat flour in Canada's Food and Drug Regulations permits up to 5% of the wheat kernel to be removed to help reduce rancidity and prolong the shelf life of whole wheat flour. The portion of the kernel that is removed for this purpose contains much of the germ and some of the bran. Such flour would comply with the Canadian regulations but would not be considered whole grain by the AACC (American Association of Cereal Chemists International) definition. Thus, in Canada, "Whole Wheat Flour" contains at least 95% of the original kernel, and "Whole Grain Whole Wheat Flour" contains 100% of the original kernel.
  
• Outside North America "whole-wheat flour" is sold as "wholemeal flour" or various type numbers or regional identifications.”