Abstract Several endemic wars have developed since the second world war. In these wars, like endemic diseases, war becomes an accepted and expected activity incorporated into the lives of a large proportion of the population. This paper illustrates some of the special problems of epidemiologic research in an endemic war based on a number of studies conducted in Lebanon over the past decade. The special problems faced by epidemiologists in an endemic war include; a situation of dynamic change where long term planning is next to impossible, the military sensitivities involved in data collection, and the compromises one has to make with scientific rigor. The paper concludes with a perspective for action by health professionals in wartime. It recommends preventive action in wartime in addition to relief and an involvement in the search for alternative approaches to conflict resolution.