The objective of this research was to determine the effect of oral minocycline on the meibomian gland nonpolar and free fatty acid lipids of chronic blepharitis patients. Patients--seborrheic blepharitis (SBBL), acne rosacea (AR) without ocular involvement, and acne rosacea with meibomianitis (AR-MKC). Minocycline treatment--50mg orally for 2 weeks followed by 100mg to the end of 3 months; this was followed by 3 more months with no treatment. Meibomian gland secretions (meibum) were collected before treatment, at the end of the 3 months on treatment, and 3 months after stopping treatment. Lipids were separated and analyzed for wax and sterol esters, triglycerides, diglycerides, free cholesterol and free fatty acids. Data were analyzed statistically by ANOVA. Minocycline treatment resulted in decreased diglycerides and free fatty acids in the group AR-MKC, which continued into the second 3 months (off treatment) and was significant. Cholesterol decreased, but triglycerides initially decreased with treatment and then increased when treatment in the group was discontinued (second 3 months); these results, however, were not significant. Thus, minocycline has its greatest effect on lipid types, which result from degradation (lipase) reactions, suggesting a lipase inhibition effect and/or direct effect on ocular flora. This minocycline effect continues even after treatment is discontinued, suggesting a more lasting effect on ocular microflora. Minocycline may be most effective when the treatment period is longer than 3 months. These results give insight into disease mechanisms associated with chronic blepharitis.