Numerous climatic conditions and individual management aspects potentially effect bioaerosol concentrations in agricultural confinement buildings. The unprecedented flooding and heavy summer rainfall of 63.0 cm during 1993 in the state of Iowa provided the opportunity to compare bioaerosol concentrations in dairy barns that used hay and feed grown under wet conditions with bioaerosol concentrations in dairy barns that used hay and feed grown with a normal rainfall of 25.5 cm. Geometric mean time-weighted average viable bioaerosol concentrations in all 40 stanchion dairy barns sampled with an all-glass impinger (AGI) were 2 x 104 cfu/m3 for yeast, 0.9 x 104 cfu/m3 for molds, 80 x 104 cfu/m3 for mesophilic bacteria, and 0.3 x 104 cfu/m3 for thermophilic bacteria. Microorganism concentrations ranged 2-3 orders of magnitude between different barns. Correlation between the variance in microorganism concentrations and climate at time of sampling, ventilation systems, individual management practices, feed type, bed materials, and barn characteristics was assessed. The proportion of variance in microorganism concentrations associated with these variables, as determined by the squared multiple correlation coefficient ranged from 31% to 45%. Important individual variables that correlated with high bioaerosol concentrations were sampling during the distribution of bedding, the use of low storage moisture feeds, and mixing fan type ventilation. Variables that were correlated with low bioaerosol concentrations were tunnel ventilation and the use of high storage moisture feeds. For the 4 classes of microorganisms studied, no correlation (all p0.20) was found with rainfall. Thus, these data refute the common assumption that in-barn use of hay and feed grown under wet conditions leads to significantly higher bioaerosol concentrations. Additional funding to continue research has been provided by the Center for Disease Control, National Institute of Occupational Safety and Health.