Background Livestock operations are under increasing pressure to fulfil minimum environmental requirements and avoid polluting the atmosphere. In regions with high farm animal densities, new farm buildings receive building permission only when biological exhaust air treatment systems (BEATS) are in place, such as biofilters. However, it is currently unknown whether BEATS can harbour pathogens such as zoonotic agents, which are potentially emitted via the purified gas. Because BEATS are located very close to the livestock building, it is assumed that BEATS‐related microorganisms are aerially transported to farm animals via the inlet system of the ventilation system. To support this hypothesis, a computer simulation was applied to calculate the wind field around a facility consisting of a virtual livestock house and an adjacent biofilter. Results Under the chosen wind conditions (speed and direction), it can be shown that turbulences and eddies may occur in the near surrounding of a livestock building with an adjacent biofilter. Consequently, this might cause the entry of the released biofilter's purified gas into the barn, including possible microorganisms within this purified gas. Conclusions If field investigations verify the results of the simulations, counter‐measures must be taken to ensure biosecurity on farms with BEATS. © 2013 Society of Chemical Industry