Lung and airway diseases caused by raw cotton, flax or hemp dust are called byssinosis. In German legislation these disorders are recognized as an occupational disease. The direct pathophysiological effects of components of the cotton itself as well as endotoxins and other concomitant factors can be involved in the development of the disease. The levels of endotoxins vary with the country of origin of the cotton and its cleanliness. Consequently, in the cotton processing industry endotoxin exposure differs markedly in different working areas, decreasing with increasing cleanliness of the cotton. Many parameters play a role in the development of byssinosis. To date there are no specific immunological markers available for diagnosis. Thus, anamnesis and exact characterization of activity and exposure circumstances at the workplace are essential. Measurement of dust levels and endotoxins may help to describe individual exposure. The current review aims to summarize the available information about byssinosis, especially with respect to endotoxins.