Asthma and allergic alveolitis account for about one third of the total number (2000 plus) of cases of work-related respiratory disease reported annually in the U.K. The majority of cases of occupational asthma are caused by chemical agents, but a significant number of the remainder result from inhalation of biological agents, such as those encountered in agriculture. A wide range of activities can result in exposure to organic dusts and associated microorganisms. These include handling mouldy hay and grains, fruit and vegetables, processing wastes, including compost making for mushroom growing and tending animals in confined facilities. To determine the incidence of occupational respiratory allergy in agriculture, to study aetiology and risk factors and, ultimately, to establish dose response relationships, requires input from a wide range of disciplines including clinicians, immunologists, microbiologists and aerobiologists. The link between what a farm worker breathes in and development of disease needs to be established. This paper reviews the role of microorganisms in the aetiology of disease with examples of typical exposures in agriculture and outlines the role that aerobiology can play in risk assessment.