Examples Minocycline is usually given by mouth (orally), but it is sometimes given as a shot (injection). It is not clear how minocycline works to reduce the activity of rheumatoid arthritis. It may work by reducing the action of certain proteins that erode cartilage. Why It Is Used Minocycline is primarily used to treat early cases of rheumatoid arthritis. If side effects still bother you and you wonder if you should keep taking the medicine, call your doctor. Do not suddenly quit taking your medicine unless your doctor tells you to. Eating yogurt that contains active cultures (lactobacillus) may help prevent some of these side effects. Taking medicine as your doctor suggests will improve your health and may prevent future problems.