Background: Fecal elastase-1 (E1) is a sensitive and reliable test in the assessment of exocrine pancreatic function in cystic fibrosis (CF). In patients with celiac disease (CD), different E1 values have been reported. E1 levels in other malabsorption conditions are unknown. Therefore, the aim of the present study was to evaluate E1 concentrations in various malabsorption syndromes., Material and Methods: The study was carried out in 54 patients, selected from patients referred with suspicion of CF, who had been diagnosed as celiac disease (CD; n = 16), secondary malabsorption syndrome (SMS, giardiasis- or cow milk-related enteropathy; n = 18) and food allergy (FA; n = 20). 70 age-matched healthy children (HC) and 131 cystic fibrosis (CF) patients served as control groups. In CD and SMS patients, a gluten-free diet was introduced. In addition, SMS patients were treated appropriately to underlying disease. In all subjects, E1 concentrations were measured. In CD and SMS patients, E1 concentrations were repeatedly measured after one year of the treatment., Results: With a cut-off level of 200 microg g-1, abnormal E1 concentrations were found in 87.2% of the CF group and in 56.2% and 50.0% of the CD and SMS subgroups, respectively. In none of FA patients, were E1 values below the normal range. After mucosal recovery, E1 concentrations in patients with CD and SMS increased, suggesting that villous atrophy can diminish exocrine pancreatic secretion. In 18 out of 19 CD and SMS patients with abnormal E1 concentrations, monitored for at least 12 months of a gluten-free diet, abnormal E1 concentrations increased above the cut-off value to normal range. Two out of the 54 referred patients were finally diagnosed as having CF, one with stable low E1 levels and the second with finally normal values., Conclusions: The exocrine pancreatic function is decreased in villous atrophy regardless of underlying disease. The specificity of the fecal elastase-1 test in the differentiation between 'primary' exocrine pancreatic insufficiency and intestinal malabsorption with mucosal atrophy is low. After mucosal regeneration, fecal elastase-1 specificity is high.