Endotoxins and allergens represent the major relevant contents of the atmospheric bioaerosol with regard to the triggering and exacerbation of allergic diseases. In this study, mattress concentrations of endotoxin and indoor allergens were measured in three hospitals in the alpine climate of Bavaria and in adjacent homes. Dust was collected from each of 10 mattresses according to a standardized protocol, and endotoxin was analyzed with the Limulus Amebocyte Lysate (LAL) test, indoor allergens Der p 1, Der f 1 and Fel d 1 were analyzed by ELISAs. The concentration of endotoxin in the mattresses did not differ significantly between different cities. The percentiles of endotoxin were significantly higher in hospitals than in homes. The concentrations of mite allergens (Der p 1 and Der f 1) in the dust were significantly lower in all hospitals than in homes. There was no significant difference of mite allergens between different time points. The concentrations of Fel d 1 were significantly higher in the autumn than in the summer (median: 1376 vs. 478ng/g). No significant differences of Fel d 1 were found between hospitals and homes or between different hospitals. As Fel d 1 concentrations reached levels at which cat allergic patients can experience symptoms, efforts had to be made to reduce the concentrations of Fel d 1 especially in hospitals. In contrast, mite allergens were low in hospitals, which can be clinically beneficial for patients with mite allergies.