Plaquenil is the brand name of hydroxychloroquine, a drug used to prevent or treat malaria. Plaquenil is also used for long-term treatment of autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythmatosis. According to the Mayo Clinic, it can take up to six months' constant use before an effect is seen in RA. Plaquenil can cause serious side effects when used in high doses for chronic diseases such as RA over the long term.

Retinal Damage

According to Drugs.com, Plaquenil given for a long term can cause retinal disorders after a few months or years of daily use--especially if the dose exceeds 400mg per day. The risk of retinal damage increases at doses of 600mg to 700mg. The New Zealand Dermatological Society recommends that to decrease the risk of retina damage, no more than 200mg of Plaquenil should be taken a day, and a dose of 400mg per day should be taken no longer than a few weeks. According to the Mayo Clinic, the daily dose for RA is based on body weight; the dose is 2.9mg per pound. This means many people taking Plaquenil for RA are taking a dose of 400mg a day or higher.

Pigment deposits in the retina can cause vision changes, according to Steven Ofner, M.D., of Eugene Oregon Eye Care. Signs of retinal damage include blurry or distorted vision, flashes of light or floaters, or loss of night vision. Retinal damage may not improve even after Plaquenil is discontinued. Dilated eye exams should be done every six months to check for retinal problems.

Neurological Disorders

According to the Mayo Clinic and New Zealand Dermatological Society, Plaquenil, given long term for diseases such as RA, can cause brain and nerve diseases such as headaches, dizziness, muscle weakness and seizures.

Blood Disorders

According to the New Zealand Dermatological Society, Plaquenil can cause abnormalities in blood counts. An abnormally low number of white blood cells can lead to infection, because white blood cells defend the body against bacteria. Low platelet count (thrombocytopenia) can lead to easy bleeding and bruising. Aplastic anemia can lead to fatigue, shortness of breath and weakness.

Hearing Disorders

In 2005, Lareb, the Netherlands Pharmacovigilance Centre, reported that it received three reports of permanent hearing loss and tinnitus after long-term Plaquenil use. The article mentioned that hydroxychloroquine is chemically related to other drugs that have known toxic effects on hearing.

Other Side Effects

Plaquenil, given over a long term to treat RA, can cause skin rashes, liver and kidney damage and stomach irritation, according to the Mayo Clinic.