The aim of this study was to assess workers' exposure to endotoxins and peptidoglycans, as well as associations between workers' reported symptoms and the detected bacterial exposures. From the filter samples, biologically-active endotoxins were analysed with the Limulus amebocyte lysate (LAL) assay. The total amount of endotoxins was analysed as 3-hydroxy (OH) fatty acids with a gas chromatography-mass spectrometry (GC-MS) assay, which was also used to assess peptidoglycans as muramic acid. Biologically-active endotoxins related better to the self-reported symptoms than total endotoxins. Specific 3-OH-14:0 fatty acid in the total endotoxin samples associated better with the symptoms than other 3-OH fatty acids. Half of the surveyed 77 workers reported respiratory symptoms, 27% eye symptoms, and 10% fever or shivering. The proportion of workers with respiratory symptoms was greater when the concentration of endotoxins was over 25 ng/m3. These endotoxin levels were occasionally found in the air of most studied occupational environments. The muramic acid concentrations of peptidoglycans were highest (medians over 100 ng/m3) in the garbage-handling plant and in the grain/vegetable storage houses. The LAL assay for endotoxins, as well as the GC-MS assay analysing muramic acid for peptidoglycans or specific 3-OH fatty acids for endotoxins, seem to be suitable methods for evaluating workers' exposure to airborne bacteria.