Organic dust is a mixture of particles originating from plants, animals, and microorganisms. Exposure to high levels of organic dust is common in many industries, but apart from that organic dust is ubiquitous in the environment with a decreasing gradient from livestock farming to large cities. Organic dust is a well-established or suspected risk factor for a range of diseases and conditions including hypersensitivity pneumonitis, toxic alveolitis, asthma, bronchitis and COPD. It is debated whether organic dust exposure is a risk factor or a preventive factor for lung cancer. On the other hand organic dust exposure seems to protect against allergic sensitisation and probably allergic asthma, allergic rhinitis and atopic dermatitis. Recently possible beneficial effects of organic dust exposure on autoimmune diseases like inflammatory bowel disease and type one diabetes have also been suggested. The impact of timing of organic exposure as well as the relation between occupational and environmental exposure to organic dust (levels as well as diversity of microorganisms) and the human microbiome will be discussed as possible explanations for the dual effects of organic dust exposure.