In this study, the microbial community within compost, emitted into the airstream, downwind and upwind from a composting facility was characterised and compared through phospholipid fatty acid (PLFA) analysis and 16S rRNA gene analysis using denaturing gradient gel electrophoresis (DGGE) and bar-coded pyrosequencing techniques. All methods used suggested that green-waste composting had a significant impact upon bioaerosol community composition. Daily variations of the on-site airborne community showed how specific site parameters such as compost process activity and meteorological conditions affect bioaerosol communities, although more data is required to qualify and quantify the causes for these variations. A notable feature was the dominance of Pseudomonas in downwind samples suggesting that this genus can disperse downwind in elevated abundances. Thirty-nine phylotypes were homologous to plant or human phylotypes containing pathogens and were found within compost, on-site and downwind microbial communities. Although the significance of this finding in terms of potential health impact was beyond the scope of this study, it clearly illustrated the potential of molecular techniques to improve our understanding of the impact that green-waste composting emissions may have on the human health.