Background/aims: Procalcitonin and C-reactive protein are two acute-phase reactant proteins, although procalcitonin is a more specific marker for bacterial infections. Procalcitonin level might also be helpful to predict the disease activity of inflammatory bowel disease. This study aimed to compare the diagnostic value of serum procalcitonin and C-reactive protein as indicators of disease activity in inflammatory bowel disease. Methods: Patients admitted to the inflammatory bowel disease inpatient clinic with suspected inflammatory bowel disease who had not yet been treated with immunosuppressive treatments were included. Disease activity, white blood cell count, sedimentation rate, serum procalcitonin and C-reactive protein levels were evaluated in 45 newly diagnosed inflammatory bowel disease patients (9 Crohn's disease and 36 ulcerative colitis). Fifty healthy volunteers were analyzed as a control group. Results: Crohn's disease patients had higher procalcitonin and C-reactive protein levels than healthy controls (Procalcitonin: 0.143 +/- 0.081 us. 0.065 +/- 0.008 ng/ml, p<0.05; C-reactive protein: 29 +/- 7.5 vs. 2.9 +/- 0.5 mg/dl, p<0.001, respectively). Ulcerative colitis patients also had slightly higher procalcitonin levels and significantly higher C-reactive protein levels than controls (Procalcitonin: 0.107 +/- 0.042 ng/ml; C-reactive protein: 23 +/- 5.5 mg/dl). Two Crohn's disease patients had procalcitonin value above 1 ng/ml. Receiver operating characteristic curve analysis demonstrated that C-reactive protein is the best marker of disease activity in inflammatory bowel disease while procalcitonin has low sensitivity and specificity. Serum procalcitonin levels were highly correlated with serum C-reactive protein but no other disease activity parameters. Conclusions: Although still within normal ranges, procalcitonin levels were slightly elevated in Crohn's disease but not in ulcerative colitis patients compared to healthy controls. Serum C-reactive protein is a reliable marker for disease activity in inflammatory bowel disease. Procalcitonin has no diagnostic value in determining disease activity.