AIMS: To assess the changes in ocular surface abnormalities and meibomian fatty acid composition in patients suffering from meibomian gland dysfunction (MGD) after treatment with oral minocycline associated with lid hygiene versus lid hygiene only. METHODS: We evaluated the break-up time, corneal staining and quality of meibomian excreta, and collected meibomian oil in 20 individuals suffering from MGD before and after 8 weeks of minocycline associated with lid hygiene (n = 10) or lid hygiene only (n = 10). Meibomian fatty acids were directly transmethylated and analysed by gas chromatography (GC) and GC mass spectrometry. RESULTS: The meibomian fatty acid composition was slightly modified after 8 weeks in both groups. The decrease in a branched-chain fatty acid (isoC20) was greater after minocycline treatment than after lid hygiene only (-65% and -25%, respectively; p<0.05). Other fatty acids were unchanged. A significant improvement in the BUT was observed after minocycline treatment (p = 0.03). CONCLUSION: This study showed better tear film stability after minocycline treatment and a biological effect on meibomian fatty acid composition in MGD patients. Minocycline was more effective than lid hygiene alone. Both interventions partly corrected fatty acid composition abnormalities. Among the fatty acids, isoC20 could be a biological marker of MGD.