SLE (Systemic Lupus Erythematosus) is an autoimmune disease which often affect women in childbearing age, and could infringe other organs as well. Since the approval of using Quinine as anti-inflammation drug for the treatment of SLE patients by the Department of Health, Executive Yuan, R.O.C (Taiwan) in May 1999, there has been a substantial increase in using the approved Quinine for treatment in SLE patients. However, does the use of Quinine for treatment in SLE patients incur side effects? The purpose of this study is to see whether the use of Quinine in SLE patients will affect the incidence of ESRD (End-Stage Renal Disease), Malignant neoplasm, Stroke, and Osteoporosis. Using a retrospective secondary data analysis approach to analyze data from the National Health Insurance Research Database (ICD-9-CM), including Registry for catastrophic illness patients (HV), Ambulatory care expenditures by visits (CD), Details of ambulatory care orders (OO), and Inpatient expenditures by admissions (DD). A total number of 1,349 new SLE patients in 1998 was selected to investigate the relationships between Quinine Medication Possession Ratio and incidence of Malignant neoplasm, ESRD, Stroke and Osteoporosis in the years of 2000 to 2007. The incidences of Malignant neoplasm, ESRD, and stroke in SLE patients who took Quinine for treatment were lower, and there is a positive correlation between Quinine Medication Possession Ratio and incidence of Malignant neoplasm and ESRD in SLE patients. But the incidence of Osteoporosis in SLE patients who took Quinine for treatment was higher. Whether the use of Quinine for treatment in SLE patients will reduce the incidences of Malignant neoplasm, ESRD, and stroke and increase the incidence of osteoporosis requires further studies.