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Background: The increase of work-related respiratory complaints in artificially ventilated buildings has multiple causes, and the role of allergen exposure and symptoms is still controversial. Study objectives: To analyze the risk factors and the association of work-related symptoms with allergen exposure and different conditions of the same air conditioning system in São Paulo, Brazil, Design: Workers were classified according to characteristics of the air conditioning system: the first group (group 1) with ventilation machinery and ducts with > 20 years of use, the second group (group 2) with ventilation machinery with > 20 years of use and ventilation ducts with < 2 years of use, and the third group (group 3) with ventilation machinery and ducts with < 2 years of use. Logistic regression was performed to check the associations between air conditioning groups, allergen exposure (fungi, mites, animal dander, and cockroach), and symptoms. Results: There was a higher prevalence of building-related worsening of respiratory symptoms (p = 0.004; odds ratio [OR], 8.53) and symptoms of rhinoconjunctivitis (p = 0.01; OR, 8.49) in group 1. There was a lower relative humidity (p = 0.05) and nonsignificant lower temperature in group 1, when compared to the other groups. The viable mold spores totals were higher outdoors than in the indoor samples (n = 45, p = 0.017). There were higher levels of Der p 1 in group 2 (p = 0.032). All allergen levels were considered low. Conclusion. There was a strong association of building-related upper-airway symptoms with places having ventilation systems with > 20 years of use.