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Recent outbreaks of highly infectious viral diseases like swine fever and avian influenza in The Netherlands have shown that despite extensive bio-security measures aiming at minimizing physical contacts between farms, disease spread could not be halted. Dust in exhaust air from swine and chicken houses may provide a favorable environment in which these viruses and other pathogenic microorganisms can survive and be transported over long distances to other farms. In a field study and in an experimental pilot-scale system, the effects of air scrubbers (bio-scrubber and acid scrubber) were tested. The field test showed higher bacterial counts in the outlet air than in the inlet air of the bio-scrubber (increase from 6.1 x 104 to 24.4 x 104 cfu/m3). An acid scrubber with sulfuric acid reduced bacteria emissions from 27 x 104 to 8.4 x 104 cfu/m3. In the pilot-scale cleaning system, different disinfectants were tested, including hydrogen peroxide, ozone, and peracetic acid. Peracetic acid gave by far the best results. It reduced bacteria and virus emissions to below detectable levels and reduced ammonia emissions by 96%. We conclude that an acid scrubber with sulfuric acid is very useful to reduce ammonia and dust emissions to the atmosphere; however, it cannot prevent the emission of pathogens. Peracetic acid reduces all these emissions, but is too costly to be used continuously. Therefore, an interesting option to prevent disease spread is to replace or supplement sulfuric acid in existing scrubbers with peracetic acid in times of high risk of disease outbreak.