Background: We retrospectively observed the results of bacteriological culture of the conjunctival swab samples before and after endoscopic nasolacrimal duct intubation to know the effect of nasolacrimal drainage recover on conjunctival contamination. Methods and Findings: 33 sides in 27 patients were included in the study. They were followed for three or more months after successful endoscopic nasolacrimal duct intubation in Department of Ophthalmology, Wakayama Medical University Hospital, Wakayama, Japan from July, 2015 to June, 2016. Bacteriological culture of the conjunctival swab samples were performed before operation and 3 months after removal of the tube of successful intubation. Conclusions: Bacteriological culture turned to negative in 5 of 9 sides (55.6%) at 3 months after removal of the tube post-successful intubation of nasolacrimal duct obstruction or stenosis. Population of Staphylococci and Candida was eliminated in conjunctiva after the successful treatment, while Corynebacterium and Streptococci were survived. Recovery of nasolacrimal drainage system was effective in diminishing bacterial growth in conjunctiva, although the effectiveness was limited.