This paper describes the outcomes of the discussion of Working Group 1. The tasks of the workgroup were to: i) review current methods for the clinical diagnosis of organic dust induced disease, and ii) suggest how further research in this field should proceed. The working group proceeded on the paradigm that for diagnosis specific and precise tests are needed, where outcomes can be related to the risk for disease. The different methods available for the investigation of individuals and groups exposed to organic dusts are summed and graded according to scientific or diagnostic values. Many of the tools should be used in experimental research only, but can be used diagnostically for evaluation during follow up of patients when treated or removed from exposure. These techniques may also be employed for investigations of outbreaks, however, only after comparison with a proper control group. Future research should focus on associations between markers of inflammation and symptoms or clinical outcomes and dose-response relationships both for short-term and long-term health effects.