Abstract Background Calprotectin, a granulocyte-derived alarmin protein, is an established noninvasive biomarker of intestinal mucosal inflammation. Fecal calprotectin testing has become the gold standard for diagnosis of inflammatory bowel diseases. The aim of this work was to determine the stability of calprotectin in stool extracts prepared with the BÜHLMANN CALEX® Cap stool preparation device. Methods The analyte stability study was carried out using CALEX® Cap extracts of human fecal left-over samples. Extraction was performed for 24 hours at room temperature and samples were aliquoted and frozen at < -20°C. The baseline calprotectin concentration was measured from thawed aliquots, which were moved to target storage temperatures (2-8 °C, 18 °C, 28 °C, and 37 °C) for up to 22 days. Five stool samples covering the measuring range of the assay were analyzed with the BÜHLMANN fCAL® turbo in four replicates. Stability evaluations were performed according to CLSI guideline EP25-A1 and EP25Ed2. Results CALEX® Cap derived extracts stored refrigerated at 2-8°C for up to 20 days and at room temperature (18-28°C) for up to 6 days demonstrated deviations from baseline of less than 20%. CALEX® Cap derived extracts stored up to 15 days at 2-8°C and up to 2 days at room temperature (18-28°C) demonstrated deviations from baseline of less than 10%. Conclusions CALEX® Cap provides a stool collection method that stabilizes fecal calprotectin concentrations for an increased processing window. This allows significant timely separation between stool collection and the actual measurement of calprotectin. This specimen stabilization provides for accurate measurements for days after sample collection and thus allows for flexibility for diagnostic laboratories.