This study comprehensively size fractionated endotoxin from compost under controlled and real-world conditions using an eight stage non-viable Andersen sampler. Detailed size fractionation helped to characterize the endotoxin, particularly as the finer fraction is more likely to travel further and penetrate deeper into the lung. Sampling was undertaken in a controlled environmental chamber where high endotoxin concentrations (>1000 EU/m3) were detected after aerosolizing a small amount of compost. It was observed that endotoxin is largely associated with a coarse size fraction, however high concentrations were also regularly detected in the fine fraction (<2.1 µm) under controlled conditions. Sampling was also undertaken at a bio-waste facility to further understanding of how endotoxin may spread and to help inform endotoxin risk modelling for nearby communities. Endotoxin sampling at a green waste compost facility was undertaken during winter months and whilst endotoxin concentrations did not appear to be significantly elevated, the highest concentrations were again observed in the coarse particulate fraction.