Common side effects of clonidine may include dry mouth, drowsiness, and fatigue. This eMedTV page lists some of the side effects that have been reported with. Clonidine is a direct-acting adrenergic agonist prescribed historically as an anti-hypertensive agent. It has found new uses, including trea. clonidine (clonidine) Side Effect Guide – warning symptoms, allergic reactions, precautions, drug interactions, overdose, missed dose, adverse effects and storage. Clonidine is a prescription medication that is used to lower blood pressure by targeting levels of certain chemicals in the blood and decreasing these levels.