Epidemiological and clinical studies have linked consumption of soy foods with low incidences of a number of chronic diseases, such as cardiovascular diseases, cancer, and osteoporosis. Over the past decades, enormous research efforts have been made to identify bioactive components in soy. Isoflavones and soy protein have been suggested as the major bioactive components in soy and have received considerable attention. However, there are hundreds of phytochemical components in soybeans and soy-based foods. In recent years, accumulating evidence has suggested that the isoflavones or soy proteins stripped of phytochemicals only reflect certain aspects of health effects associated with soy consumption. Other phytochemicals, either alone or in combination with isoflavones or soy protein, may be involved in the health effects of soy. This review attempts to summarize major non-isoflavone phytochemicals in soy, as well as their bioavailability and health effects. In addition, a brief discussion of components formed during food processing is also included.