Background: Antibodies to saccharomyces cerevisiae (ASCA), antibodies to perinuclear anti-neutrophil cytoplasmic (pANCA), pancreatic autoantibodies (PAB) and antibodies against intestinal goblet cells (GAB) are important in diagnosing Crohn's disease (CD) and ulcerative colitis (UC). However, little is known about their diagnostic value in real clinical practice in China. This retrospective study aimed to present our 2-year clinical experience with those biomarkers in diagnosis of CD and UC. Methods: A total of 140 patients with UC, 128 patients with CD, and 224 patients with intestinal associated diseases as disease controls were included. Serum ASCA were determined by ELISA. Serum pANCA, GAB, and PAB were tested by indirect immunofluorescent assay. Retrospective review of laboratory results and clinical information was performed. Results: ASCA and ASCA +/pANCA - showed poor abilities in differentiating CD from UC, CD from intestinal Behcet's disease (BD), or CD from intestinal tuberculosis (ITB). In contrast, PAB exhibited good capacities in differentiating CD from UC, CD from intestinal BD, and CD from ITB. IgG pANCA demonstrated a high sensitivity and specificity in differentiating UC from CD. pANCA +/ASCA - or pANCA +/PAB - displayed a high sensitivity and specificity in differentiating UC from CD. GAB showed poor potential in differentiating UC from CD. PAB were positively correlated with early disease onset, ileocolonic disease, and perianal disease in CD patients. Conclusions: Our data suggest that pANCA and PAB are helpful in diagnosis of UC and CD, respectively, while ASCA and GAB were not. Our findings indicate a clear need for additional biomarkers for diagnosis of CD in China.