Objective To analyze the clinical characteristics of systemic lupus erythematosus (SLE) first presenting digestive system symptoms. Methods With retrospective analysis, choose gastroenterology department hospitalized patients presenting agnogenic abdominal pain, diarrhea and so on digestive system symptoms, finally diagnosed as SLE from July 2004 to June 2009 as study group. According to case number ratio 1 to 2, SLE patients in rheumatology department with fever,arthralgia, and rash chief complain were selected randomly as control group at same period. The clinical characters were compared in the two groups. Results A total of 31 SLE patients (27 female)in study group and 62 patients (55 female) in control group were collected. The data analyzed by the logistic multivariate analysis method, it was suggested that abdominal pain (OR= 7.91) and diarrhea (OR=6.26) were the most common symptoms in the study group. The course was longer (OR=1.41) and weight loss was more severe (OR = 1. 37) than the control group before diagnosis,however, the increase of erythrocyte sedimentation rate (OR= 0. 88) and the positive rate of urinary red cells was less obvious (OR=0. 56). Conclusions SLE patient first presenting digestive system symptoms should be noted and identified in clinical practice to reduce misdiagnosis and missed diagnosis.