Objective of the Study: Calprotectin plays a crucial role in the diagnosis of inflammatory bowel diseases. Measuring the concentration of fecal calprotectin reduces the need for invasive procedures. The objective of this study is to measure the concentration of calprotectin using two different immunochemical methods and to perform a detailed comparison and analysis of the results obtained from these measurements. Study Design: This research was conducted as a cross-sectional study. Subjects and Methods: The study, conducted in July 2024 at the Clinical Institute for Laboratory Diagnostics at the University Hospital Center Osijek, included 30 stool samples from inpatient and outpatient subjects for the measurement of fecal calprotectin concentration. The study involved patients of various age groups and both genders. The concentration of fecal calprotectin was measured using two immunochemical analyzers, BIO-FLASH® (Biokit, S.A) and OC-SENSOR™ Ceres (EIKEN CHEMICAL Co., LTD., Tokyo, Japan). Results: An excellent correlation between the methods was determined using Spearman's correlation coefficient. The Passing-Bablok regression analysis revealed constant and proportional discrepancies between the methods. The Bland-Altman analysis showed a statistically significant difference between the two methods. Conclusion: The analysis demonstrated a significant difference between the two methods, indicating that unexpected results should be further examined with additional tests.