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In-barn manure separation systems are becoming very popular due to various environmental pressures on the swine industry. According to the literature, a separation of the feces and the urine directly underneath the slats should have a positive impact on the barn air quality. From an occupational health and safety perspective, the maximum endotoxin and total bacteria concentrations to ensure the worker safety should not exceed 300 endotoxin unit per cubic meter of air (EU/m) and 104 colony-forming unit per cubic meter of air (CFU/m), respectively. In the current study, the effect on air quality of six in-barn manure handling systems has been measured. A flat scraper system and four separation systems installed underneath the slats (a conveyor belt system, a conveyor net system and a V-shaped scraper operated at two frequencies of operation) were evaluated and compared to a conventional pull-plug system (control). The experiment took place in twelve independent and identical chambers housing four growers-finisher pigs each and air samples were collected and analyzed for total dust, endotoxin, bacteria, and mould counts. The data analysis shows that on average, dust, endotoxin, bacteria and mold emissions from the pull-plug chambers were 23.60 mg/day-kgpig, 0.69 EU/s-kgpig, 33.90 CFU./s-kgpig and 0.88 CFU/s-kgpig, respectively. These emissions were not significantly affected by the treatments. Compared to the control (pullplug system), the Cemagref net and daily V-shaped scraper reduced the dust emissions by 9% and 4%. Also, overall, only the Cemagref net and daily V-shaped scraper reduced all endotoxin, bacteria and mould emissions by an average of 20% and 5%, respectively.