Background: The serum zinc concentration is frequently applied for the assessment of zinc deficiency, but this concentration is also influenced by other factors. The aim of this study was to compare various methods of assessing the zinc status in patients with Crohn's disease. Methods: Serum levels of zinc, serum alkaline phosphatase activity, and zinc in various types of cells were related to factors potentially inducing zinc deficiency: the number of liquid stools, weight loss, bowel resection, and the extent and severity of inflammation. Results: Thirty-one patients with more or less active Crohn's disease were included. In 68% of these patients the serum zinc concentration was less than the reference level, and it was correlated with the extent of bowel resection and the van Hees Index but not with the Crohn's Disease Activity Index. Serum alkaline phosphatase activity was correlated with bowel resection. Zinc in blood cells was poorly correlated with factors inducing zinc deficiency. Conclusion: A decrease of serum zinc concentration is frequently seen in active Crohn's disease. This study suggests that the determination of zinc in blood cells is not superior to the determination of the serum zinc concentration and serum alkaline phosphatase activity.