Research Motivation: Gastroesophageal reflux disease (GERD) is a well-recognised cause of respiratory symptoms in children. Confirming a diagnosis of reflux aspiration remains difficult, due to limitations in currently available investigations. The presence of pepsin in respiratory secretions has been documented in literature as a marker of reflux aspiration; however the correlation of pepsin assay results with clinical outcomes has not previously been reported. Aim: This study investigates the way in which results of pepsin assays influence the management of children with suspected reflux aspiration, as well as clinician attitudes towards pepsin assay. Methodology: Retrospective chart review of 318 patient records from January 2005 -December 2009, at Sydney Children's Hospital. Pepsin assay results were compared with results from other standard investigations for GERD. Findings: Children with GERD and respiratory symptoms were 1.8 times as likely to be positive for pepsin compared to children without respiratory symptoms (OR 1.8, 95% C.I. = 1.09 -2.96). A significantly greater quantity of pepsin was detected in tracheal aspirates of children with GERD and respiratory symptoms compared to those without (median 43, 0-996FU, p=0.002). In children with GERD and respiratory symptoms, pepsin assay, unlike standard GERD investigations was the only tool found to have statistical significance as a marker of possible reflux aspiration. Clinicians found the pepsin assay to be useful in the management of children with suspected reflux aspiration. Implications: The findings of this study show that the pepsin assay helps in the assessment of children with GERD and respiratory symptoms in who reflux aspiration are suspected.