In clinical routine, antibiotic eye drops are frequently used, mostly for the therapy of bacterial infections as well as for infection prophylaxis after surgery. Due to the anatomical connection through the nasolacrimal duct, there is the possibility that antibiotic eye drops also have an influence on the nasal and pharyngeal microbiome. This was investigated in the present study by a one-week instillation period with two different commonly used antibiotic eye drops.