To study the effect of exposure to low levels of bioaerosols on PEFmonitoring and antibody responses, five groups of waste collectors from different areas in Denmark were investigated. The five groups handled different kinds of waste using different kinds of organisation logistics and collection equipment. One group worked with a new, experimental system (“System 2000”), which involved source separation of waste into compostable and residual fractions. Waste collectors exposed to “high” (maximum of 72 EU/m3) levels of endotoxins had significantly (p < 0.001) higher serum concentrations of IgG than waste collectors exposed to “low” levels of endotoxins. Working with “System 2000” resulted in significantly higher serum concentrations of IgG (p < 0.001) and IgA (p < 0.01). Peak flow variability appeared to be significantly affected by exposure to Aspergillus fumigatus. It is concluded that the changes in peak flow variability and the elevated concentrations of immunoglobulins may be used as indicators of sub-clinical effects of relatively low exposure to organic dust. Assessment of peak flow variability (or serum IgG concentrations) may be used in surveillance systems to prevent clinical symptoms caused by organic dust exposure.