This preliminary study quantified the levels of airborne dust and endotoxins present in pig confinement buildings. The dust was separated into three size fractions, ≤ 3.5, ≤ 8.5 and < 51.2 μm, using cyclone pre-separators and a modified cassette holder for total dust. The results indicate that there is a large day-to-day variation in total dust determined in a single confinement building and that the smallest fraction ≤ 3.5 μm varies from building to building but not in a single building. The levels of endotoxin determined in this study were similar to those found in other studies but indicated that there is a significant enrichment of endotoxin in the size fraction 3.5–8.5 μm. The implications from this are that the assessment of the potential health risk to the farmer from endotoxin present in the airborne dust must be assessed using a biologically relevant criterion based on particle penetration into the thoracic region of the exposed farmer's lung. The current methods of looking at endotoxin levels in respirable and total dust give little information in regard to the potential health risk.