Farmer's lung disease (FLD) is common in eastern France. It is the main form of occupational hypersensitivity pneumonitis, caused by chronic inhalation of microorganisms (antigens) from mouldy hay, straw, or grain. The purpose of this study was to assess, with a panel of data collected between 1997-2003, environmental factors and agricultural practices that independently modify concentrations in hay of microorganisms potentially responsible for FLD. A total of 629 hay samples from 86 farms were included in statistical analyses using linear multilevel regression models allowing to consider the nested structure of the data: individual-level (batch of hay) and group-level (farm). The outcome variable of these models was the concentration in hay (logarithmic value of concentration+1) of microorganisms incriminated in FLD (Absidia corymbifera, Eurotium spp., thermophilic actinomycetes). The simultaneous analysis of batch of hay- and farm-level factors showed that bad climatic conditions of harvest, high-density hay-packing modes, (especially round bales) and altitude (2nd plateau, ]700-900] m) were the main factors associated with high concentrations of these microorganisms in hay. This study allowed clarification of the factors that influence the microbial concentration of hay with etiological agents of FLD.