Two exemplary investigations with different questions were carried out in Munich and Stuttgart by sampling bio-aerosols due to and during the collection and emptying of different types of waste bins. The emissions were regarded qualitatively and quantitatively, in order to answer the question, whether and to which amount differences of bio-aerosol emissions occurred due to the kind of wastes collected. The lowest emissions of airborne microorganisms were found during the collection of the paper waste fraction. In comparison, the amounts of them during the collection of unseparated household wastes as well as source separated bio-wastes and the remaining residual waste fraction were higher. Between the three latter, no significant differences could be found, only a tendency of higher values for the thermotolerant mould A. fumigatus during the collection of bio- and residual wastes was observed. Maybe this was caused by special features of the different sampling locations, but it could also be due to the longer collection intervals (bio- and residual wastes were partially collected every two weeks, unseparated wastes every week).