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Objective Goat farming is a rapidly expanding livestock sector with a unique husbandry system. Little is known about related occupational exposures and health risks. We aimed to 1) assess occupational exposure to particulate matter, endotoxin and airborne pathogens; and 2) characterize goat farmers’ respiratory health based on their upper airway microbiome and fungal sensitization profiles.Material and Methods Repeated personal exposure sampling was performed for 41 goat farmers; particulate matter concentrations were measured gravimetrically and endotoxins were quantified by LAL-assay. Airborne microbiota were characterized from 15 farms using 16S rRNA-gene sequencing. Health assessments were performed with 93 goat farmers and evaluated against findings from 200 non-farming neighboring residents. Nasopharyngeal and oropharyngeal swabs were analyzed by qPCR for 35 respiratory pathogens and by 16S rRNA-gene sequencing for microbiota composition. Serum samples were evaluated by ELISA for antibody titers against fungal antigens.Results Exposure to particulate matter and endotoxin was prominent, 90% of measurements exceeded the Dutch occupational exposure limit for endotoxin (90 EU/m³). Goat farms harbored large varieties of airborne micro-organisms, including potential respiratory pathogens. Compared to non-farming residents, qPCR indicated elevated prevalence of Salmonella spp. (17.6%) and Staphylococcus aureus (49.5%) among farmers. Respiratory microbiota analysis revealed higher diversity among farmers with increased abundances of Lactococcus, Stenotrophomonas, Fusobacterium, and Micrococcus spp. Farmers also exhibited higher sensitization rates to fungal species relevant to hypersensitivity pneumonitis, particularly Aspergillus spp.Conclusion Goat farmers experience significant occupational exposures to airborne micro-organisms and their components, posing both infectious and non-infectious respiratory health risks. Overall, our findings underscore the need for improved occupational health protection and support targeted interventions to reduce microbial air pollution in goat farming.Funding This research is funded by the Ministry of Health, Welfare and Sport and the Ministry of Agriculture, Nature and Food Quality of The Netherlands.