Homogenized milk is processed to break down the fat so that the milk is more consistent, whereas whole (or raw) milk has not gone through this process, resulting in solids rising to the surface over time. The process is done to make milk more enjoyable to drink for most people, and it is typically a feature of milk sold in supermarkets. The phrase "whole milk" in this case refers to raw, unprocessed milk, rather than the more common usage which refers to the milk's fat content.
The homogenization process generally occurs just prior to the milk being pasteurized. This reduces the risk of the larger milk fat clumps turning sour during the pasteurization process. Though often debated by natural health advocates, according to the Centers for Disease Control, the nutritional difference between whole milk and those that have been homogenized and pasteurized is negligible, despite the small amount of enzymes that are lost during pasteurization. The main issue is that unpasteurized whole milk has a much higher risk of containing harmful bacteria, which can cause severe illness or even death in some cases.
Pasteurization is the process that causes the biggest change in the milk sold in stores. In this process, the milk is heated to a high temperature, then quickly cooled down again, which helps to eliminate the potential illness causing bacteria found in milk. It also adds to the longevity of the product, as pasteurized milk lasts longer on shelves by weeks or even months. For safety reasons, many states have regulations in place restricting the sale of raw, whole milk and federal laws are in place to prevent it from being packaged for consumers to be sold across state lines.