Because consumer products release them, polybrominated diphenyl ethers (PBDEs) are frequently present in a variety of indoor environments including homes and workplaces. Our goal was to investigate PBDEs contamination of workplace air-conditioner filter dust to assess the health effects of contaminated dust on workers with occupational exposure. Nine medical clinics, four dental clinics, eight factory offices, and six factory clean rooms were selected in southern Taiwan between April 2013 and September 2014. Air-conditioner-filter dust was collected by a high-efficiency vacuum cleaner and then PBDEs were analyzed by a high-resolution gas chromatography coupled with high-resolution mass spectrometry. The Σ14PBDEs (the sum of BDE-28, 47, 99, 100, 153, 154, 183, 196, 197, 203, 206, 207, 208, and 209) in independent-air-conditioner filter (IAF) dust was not significantly lower in dental clinics (736 ng g–1) than in medical clinics (1600 ng g–1) and electronic plant offices (2570 ng g–1). PBDEs level was distinctly higher by an order of magnitude in central-air-conditioner system filter (CASF) dust in clean rooms (32,600 ng g–1), than in IAF dust. In clinic and the office workers, PBDEs daily intake via indoor dust ingestion varied from 2.96 × 10–8 to 1.25 × 10–7 mg kg b.w.–1 day–1 (29.6–125 ng kg b.w.–1 day–1), which was obviously below the lowest observed adverse effect of level (LOAEL) of 1 mg kg b.w.–1 day–1. Assessment of the risk of non-cancer diseases with neurobehavioral effects and of cancer with neurobehavioral effects in clinic and office workers was notably below threshold values (non-cancer: 1.00 and cancer: 1.00 × 10–6). In conclusion, clinic and office workers had no harmful effects in the currently existing levels of indoor dust PBDEs in workplaces. IAF or CSAF dust can possibly reflect spatial and temporal dust distribution in the microenvironment. It is also suggested that collection of air-conditioner filter dust may be an alternative method to conventional dust sampling for assessment of indoor contamination by PBDEs.