Chronic dacryocystitis affects tear film functionality and can predispose to ocular surface disease, however the specific effect of chronic dacryocystitis on meibomian gland function has not been studied. This group therefore performed in vivo confocal microscopy in 28 patients’ eyes on the side affected by dacryocystitis and compared to their fellow eye and also to 27 healthy control patients. The participants also completed an Ocular Surface Disease Index questionnaire, had tear break up time measured and a Schirmer test. The confocal microscopy parameters included acinar unit density and diameter as well as periglandular inflammatory cell density. The study showed a significant reduction in acinar density, and raised inflammatory cells and shortest diameter of meibomian glands but no difference in their diameter – perhaps because they were obliterated vertically but blocked and therefore distended horizontally. The confocal microscopy parameters showed a strong correlation between dacrycocystistis and poor gland function. This study demonstrates that chronic dacryocystitis has a detrimental effect on meibomian gland function on the affected side, suggesting that treatment of underlying disease should be considered a priority.