Objective Epidemiologic studies comparing the incidence and prevalence of systemic lupus erythematosus (SLE) and isolated cutaneous lupus erythematosus (CLE) are few. Olmsted County, Minnesota provides a unique setting for such a study owing to resources of the Rochester Epidemiology Project. We sought to describe and compare the incidence and prevalence of SLE and CLE from 1993 to 2005. Methods SLE cases were identified from review of medical records and fulfilled the 1982 ACR classification criteria. CLE cases included patients with classic discoid LE (CDLE), subacute cutaneous LE (SCLE), lupus panniculitis and bullous LE. Age-and sex-adjusted incidence and prevalence were standardized to 2000 US white population. Results The age- and sex-adjusted incidence of SLE (2.9 per 100,000; 95% CI 2.0, 3.7) was similar to that of CLE (4.2 per 100,000; 95% CI 3.1, 5.2, p= 0.10). However, incidence of CLE was three times higher than SLE in males (2.4 versus 0.8 per 100,000, p=0.009). The age- and sex-adjusted prevalence of CLE on January 1, 2006 was higher than that of SLE (70.4 versus 30.5 per 100,000; p<0.001). The prevalence of CLE and SLE in women were similar but the CLE prevalence was higher in men than in women (56.9 versus 1.6 per 100,000, p<0.001). The incidence of CLE rose steadily with age and peaked at 60-69 years. Conclusion The incidences of CLE and SLE are similar but CLE is more common than SLE in males and in older adults. These findings may reflect differences in genetic or environmental etiology of CLE.