Diets rich in vegetables and fruits are known to be protective against several diseases. Only a limited number of vegetables and fruits are consumed as part of the daily diet in Western countries. Historically, indigenous vegetables and fruits are known for their medicinal and nutritional value in countries where they were originated and/or domesticated. However, relatively few systemic studies and reviews were conducted to enumerate the potential of these vegetables to human health benefits. Although certain indigenous crops have received attention, the majority of these crops with strong potential biological activities were neglected and/or not reported. Considering the current health-related problems and obesity-related diseases, it is timely to enumerate the health-promoting properties of certain indigenous vegetables. In this report, we have reviewed some of the important crops indigenous to Southeast Asia and their potential health-promoting properties.