Although [99mTc]HMPAO-labeled leukocyte scintigraphy is widely used in the assessment of IBD, the time point chosen for imaging is still controversial. The aim of the present study was to determine the optimal scanning sequence to assess IBD extension and activity. Sixty-two consecutive patients with active and 18 with inactive IBD were prospectively studied. Clinical evaluation, colonoscopy, radiology, and scintigraphy were performed within three days, without changes in the patient's treatment. Compared to early scan (45 min), late scan (3 hr) had a higher sensitivity (85% vs 100%) and accuracy (85% vs 95%) in identifying patients with active IBD and in defining IBD extension. Combinations of values from both scans did not improve accuracy of scintigraphy, which is lower in Crohn's disease than in ulcerative colitis and also in patients receiving steroid treatment. In conclusion, a single late scintigraphy scan provides the best means to identify patients with active IBD and to assess disease extension.