Thyroid problems are common in people with lupus. According to statistics from the Johns Hopkins Lupus Center, about 6 percent of people with lupus have underactive thyroid, or hypothyroidism, and 2 percent have overactive thyroid, or hyperthyroidism. A 2009 study published in the Journal of Clinical Rheumatology found that just over 6 percent of those with lupus tested had thyroid problems caused by autoimmune thyroid disease, compared to 2 percent in the general population.